| showdb

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Display information on configured databases

## Description

showdb displays a table with the names, contents and access methods of the sequence databases configured for your EMBOSS installation.

## Usage

Here is a sample session with showdb

Display information on the currently available databases:

    % showdb
    Display information on configured databases

    # Name            Type                          Comment
    # =============== ============================= =======
    bpsw              Protein,Protfeatures          BioPerl OBDA index of test SwissProt
    bpworm            Protein                       BioPerl OBDA index of test wormpep fasta file
    qapblast          Protein                       BLAST swissnew
    qapblastall       Protein                       BLAST swissnew, all fields indexed
    qapblastsplit     Protein                       BLAST swissnew split in 5 files
    qapblastsplitexc  Protein                       BLAST swissnew split in 5 files, not file 02
    qapblastsplitinc  Protein                       BLAST swissnew split in 5 files, only file 02
    qapfasta          Protein                       FASTA file swissnew entries
    qapflat           Protein,Protfeatures          SpTrEmbl flatfile
    qapflatall        Protein,Protfeatures          SpTrEmbl flatfiles, all fields indexed
    qapir             Protein,Protfeatures          Test PIR indexed by dbigcg
    qapirall          Protein,Protfeatures          Test PIR indexed by dbigcg with fields
    qapirexc          Protein,Protfeatures          Test PIR indexed by dbigcg except file pir1
    qapirinc          Protein,Protfeatures          Test PIR indexed by dbigcg file pir1
    qapxfasta         Protein                       FASTA file swissnew entries
    qapxflat          Protein                       Swissnew flatfiles
    qasrswww          Protein,Protfeatures          Remote SRS web server
    qaxpir            Protein,Protfeatures          PIR indexed by dbxgcg
    qaxpirall         Protein,Protfeatures          Test PIR indexed by dbxgcg with fields
    qaxpirexc         Protein,Protfeatures          Test PIR indexed by dbxgcg except pir1
    qaxpirinc         Protein,Protfeatures          Test PIR indexed by dbxgcg file pir1
    tpir              Protein                       Test PIR using NBRF access for 4 files
    tsw               Protein,Protfeatures,Text     Swissprot native format with EMBL CD-ROM index
    tswnew            Protein,Protfeatures          SpTrEmbl as 3 files in native format with EMBL CD-ROM index
    bpembl            Nucleotide,Nucfeatures        BioPerl OBDA index of test EMBL
    bpgb              Nucleotide,Nucfeatures        BioPerl OBDA index of test GenBank
    ena               Nucleotide,Nucfeatures        ENA via URL
    qanfasta          Nucleotide                    FASTA file EMBL rodents
    qanfastaall       Nucleotide                    FASTA file EMBL rodents, all fields indexed
    qanflat           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanflatall        Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanflatexc        Nucleotide,Nucfeatures        EMBL flatfiles, no rodent file
    qanflatinc        Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
    qangcg            Nucleotide,Nucfeatures        GCG format test EMBL
    qangcgall         Nucleotide,Nucfeatures        GCG format test EMBL
    qangcgexc         Nucleotide,Nucfeatures        GCG format test EMBL without prokaryotes
    qangcginc         Nucleotide,Nucfeatures        GCG format test EMBL only prokaryotes
    qanxfasta         Nucleotide                    FASTA file EMBL rodents
    qanxfastaall      Nucleotide                    FASTA file EMBL rodents, all fields indexed
    qanxflat          Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanxflatall       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields indexed
    qanxflatexc       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file
    qanxflatinc       Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
    qanxgcg           Nucleotide,Nucfeatures        GCG format EMBL
    qanxgcgall        Nucleotide,Nucfeatures        GCG format EMBL indexed by dbxgcg with query fields
    qanxgcgexc        Nucleotide,Nucfeatures        GCG format EMBL without prokaryotes
    qanxgcginc        Nucleotide,Nucfeatures        GCG format EMBL only prokaryotes
    qawfasta          Nucleotide                    FASTA file wormpep entries
    qawxfasta         Nucleotide                    FASTA file wormpep entries
    qaxembl           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    tembl             Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL CD-ROM index
    temblall          Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index
    temblrest         Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index
    temblvrt          Nucleotide,Nucfeatures        EMBL in native format with EMBL CD-ROM index
    tensembldasgrch37 Nucleotide                    Homo_sapiens Reference server based on GRCh37 assembly
    testdb            Nucleotide                    test sequence data
    tgb               Nucleotide,Nucfeatures        Genbank by SRS at DKFZ
    tgenbank          Nucleotide,Nucfeatures        Test GenBank in native format with EMBL CD-ROM index
    tgenedashuman     Nucleotide                    The Ensembl human Gene_ID reference source
    tflybase          Features                      Flybase CHADO server
    tgenedb           Features                      GeneDb CHADO server
    ttax              Taxonomy                      NCBI taxonomy test data
    taxon             Taxonomy                      NCBI taxonomy
    drcat             Resource                      Data Resource Catalogue
    tedam             Obo                           Test EDAM using dbxedam test indexes
    tobo              Obo                           Test EDAM using dbxobo test indexes
    chebi             Obo                           Chemical Entities of Biological Interest
    eco               Obo                           Evidence code ontology
    edam              Obo                           EMBRACE Data and Methods ontology
    edam_data         Obo                           EMBRACE Data and Methods ontology (data)
    edam_format       Obo                           EMBRACE Data and Methods ontology (formats)
    edam_identifier   Obo                           EMBRACE Data and Methods ontology (identifiers)
    edam_operation    Obo                           EMBRACE Data and Methods ontology (operations)
    edam_topic        Obo                           EMBRACE Data and Methods ontology (topics)
    go                Obo                           Gene Ontology
    go_component      Obo                           Gene Ontology (cellular components)
    go_function       Obo                           Gene Ontology (molecular functions)
    go_process        Obo                           Gene Ontology (biological processes)
    pw                Obo                           Pathways ontology
    ro                Obo                           Relations ontology
    so                Obo                           Sequence ontology
    swo               Obo                           Software ontology

Example 2

Write the results to a file:

    % showdb -outfile showdb.out
    Display information on configured databases

Go to the output files for this example

Example 3

Display information on one explicit database:

    % showdb -database tsw
    Display information on configured databases

    # Name         Type                      Comment
    # ============ ========================= =======
    tsw            Protein,Protfeatures,Text Swissprot native format with EMBL CD-ROM index

Go to the input files for this example

Example 4

Display information on the databases formatted in HTML:

    % showdb -html
    Display information on configured databases

    NameTypeComment
    bpswProtein ProtfeaturesBioPerl OBDA index of test SwissProt
    bpwormProteinBioPerl OBDA index of test wormpep fasta file
    qapblastProteinBLAST swissnew
    qapblastallProteinBLAST swissnew, all fields indexed
    qapblastsplitProteinBLAST swissnew split in 5 files
    qapblastsplitexcProteinBLAST swissnew split in 5 files, not file 02
    qapblastsplitincProteinBLAST swissnew split in 5 files, only file 02
    qapfastaProteinFASTA file swissnew entries
    qapflatProtein ProtfeaturesSpTrEmbl flatfile
    qapflatallProtein ProtfeaturesSpTrEmbl flatfiles, all fields indexed
    qapirProtein ProtfeaturesTest PIR indexed by dbigcg
    qapirallProtein ProtfeaturesTest PIR indexed by dbigcg with fields
    qapirexcProtein ProtfeaturesTest PIR indexed by dbigcg except file pir1
    qapirincProtein ProtfeaturesTest PIR indexed by dbigcg file pir1
    qapxfastaProteinFASTA file swissnew entries
    qapxflatProteinSwissnew flatfiles
    qasrswwwProtein ProtfeaturesRemote SRS web server
    qaxpirProtein ProtfeaturesPIR indexed by dbxgcg
    qaxpirallProtein ProtfeaturesTest PIR indexed by dbxgcg with fields
    qaxpirexcProtein ProtfeaturesTest PIR indexed by dbxgcg except pir1
    qaxpirincProtein ProtfeaturesTest PIR indexed by dbxgcg file pir1
    tpirProteinTest PIR using NBRF access for 4 files
    tswProtein Protfeatures TextSwissprot native format with EMBL CD-ROM index
    tswnewProtein ProtfeaturesSpTrEmbl as 3 files in native format with EMBL CD-ROM index
    bpemblNucleotide NucfeaturesBioPerl OBDA index of test EMBL
    bpgbNucleotide NucfeaturesBioPerl OBDA index of test GenBank
    enaNucleotide NucfeaturesENA via URL
    qanfastaNucleotideFASTA file EMBL rodents
    qanfastaallNucleotideFASTA file EMBL rodents, all fields indexed
    qanflatNucleotide Nucfeatures RefseqEMBL flatfiles
    qanflatallNucleotide Nucfeatures RefseqEMBL flatfiles
    qanflatexcNucleotide NucfeaturesEMBL flatfiles, no rodent file
    qanflatincNucleotide NucfeaturesEMBL flatfiles, only rodent file
    qangcgNucleotide NucfeaturesGCG format test EMBL
    qangcgallNucleotide NucfeaturesGCG format test EMBL
    qangcgexcNucleotide NucfeaturesGCG format test EMBL without prokaryotes
    qangcgincNucleotide NucfeaturesGCG format test EMBL only prokaryotes
    qanxfastaNucleotideFASTA file EMBL rodents
    qanxfastaallNucleotideFASTA file EMBL rodents, all fields indexed
    qanxflatNucleotide Nucfeatures RefseqEMBL flatfiles
    qanxflatallNucleotide Nucfeatures RefseqEMBL flatfiles, all fields indexed
    qanxflatexcNucleotide Nucfeatures RefseqEMBL flatfiles, no rodent file
    qanxflatincNucleotide NucfeaturesEMBL flatfiles, only rodent file
    qanxgcgNucleotide NucfeaturesGCG format EMBL
    qanxgcgallNucleotide NucfeaturesGCG format EMBL indexed by dbxgcg with query fields
    qanxgcgexcNucleotide NucfeaturesGCG format EMBL without prokaryotes
    qanxgcgincNucleotide NucfeaturesGCG format EMBL only prokaryotes
    qawfastaNucleotideFASTA file wormpep entries
    qawxfastaNucleotideFASTA file wormpep entries
    qaxemblNucleotide Nucfeatures RefseqEMBL flatfiles
    temblNucleotide Refseq NucfeaturesEMBL in native format with EMBL CD-ROM index
    temblallNucleotide Nucfeatures RefseqEMBL in native format with EMBL CD-ROM index
    temblrestNucleotide Nucfeatures RefseqEMBL in native format with EMBL CD-ROM index
    temblvrtNucleotide NucfeaturesEMBL in native format with EMBL CD-ROM index
    tensembldasgrch37NucleotideHomo_sapiens Reference server based on GRCh37 assembly
    testdbNucleotidetest sequence data
    tgbNucleotide NucfeaturesGenbank by SRS at DKFZ
    tgenbankNucleotide NucfeaturesTest GenBank in native format with EMBL CD-ROM index
    tgenedashumanNucleotideThe Ensembl human Gene_ID reference source
    tflybaseFeaturesFlybase CHADO server
    tgenedbFeaturesGeneDb CHADO server
    ttaxTaxonomyNCBI taxonomy test data
    taxonTaxonomyNCBI taxonomy
    drcatResourceData Resource Catalogue
    tedamOboTest EDAM using dbxedam test indexes
    toboOboTest EDAM using dbxobo test indexes
    chebiOboChemical Entities of Biological Interest
    ecoOboEvidence code ontology
    edamOboEMBRACE Data and Methods ontology
    edam_dataOboEMBRACE Data and Methods ontology (data)
    edam_formatOboEMBRACE Data and Methods ontology (formats)
    edam_identifierOboEMBRACE Data and Methods ontology (identifiers)
    edam_operationOboEMBRACE Data and Methods ontology (operations)
    edam_topicOboEMBRACE Data and Methods ontology (topics)
    goOboGene Ontology
    go_componentOboGene Ontology (cellular components)
    go_functionOboGene Ontology (molecular functions)
    go_processOboGene Ontology (biological processes)
    pwOboPathways ontology
    roOboRelations ontology
    soOboSequence ontology
    swoOboSoftware ontology

Example 5

Display protein databases only:

    % showdb -nonucleic
    Display information on configured databases

    # Name            Type                          Comment
    # =============== ============================= =======
    bpsw              Protein,Protfeatures          BioPerl OBDA index of test SwissProt
    bpworm            Protein                       BioPerl OBDA index of test wormpep fasta file
    qapblast          Protein                       BLAST swissnew
    qapblastall       Protein                       BLAST swissnew, all fields indexed
    qapblastsplit     Protein                       BLAST swissnew split in 5 files
    qapblastsplitexc  Protein                       BLAST swissnew split in 5 files, not file 02
    qapblastsplitinc  Protein                       BLAST swissnew split in 5 files, only file 02
    qapfasta          Protein                       FASTA file swissnew entries
    qapflat           Protein,Protfeatures          SpTrEmbl flatfile
    qapflatall        Protein,Protfeatures          SpTrEmbl flatfiles, all fields indexed
    qapir             Protein,Protfeatures          Test PIR indexed by dbigcg
    qapirall          Protein,Protfeatures          Test PIR indexed by dbigcg with fields
    qapirexc          Protein,Protfeatures          Test PIR indexed by dbigcg except file pir1
    qapirinc          Protein,Protfeatures          Test PIR indexed by dbigcg file pir1
    qapxfasta         Protein                       FASTA file swissnew entries
    qapxflat          Protein                       Swissnew flatfiles
    qasrswww          Protein,Protfeatures          Remote SRS web server
    qaxpir            Protein,Protfeatures          PIR indexed by dbxgcg
    qaxpirall         Protein,Protfeatures          Test PIR indexed by dbxgcg with fields
    qaxpirexc         Protein,Protfeatures          Test PIR indexed by dbxgcg except pir1
    qaxpirinc         Protein,Protfeatures          Test PIR indexed by dbxgcg file pir1
    tpir              Protein                       Test PIR using NBRF access for 4 files
    tsw               Protein,Protfeatures,Text     Swissprot native format with EMBL CD-ROM index
    tswnew            Protein,Protfeatures          SpTrEmbl as 3 files in native format with EMBL CD-ROM index
    tflybase          Features                      Flybase CHADO server
    tgenedb           Features                      GeneDb CHADO server
    ttax              Taxonomy                      NCBI taxonomy test data
    taxon             Taxonomy                      NCBI taxonomy
    drcat             Resource                      Data Resource Catalogue
    tedam             Obo                           Test EDAM using dbxedam test indexes
    tobo              Obo                           Test EDAM using dbxobo test indexes
    chebi             Obo                           Chemical Entities of Biological Interest
    eco               Obo                           Evidence code ontology
    edam              Obo                           EMBRACE Data and Methods ontology
    edam_data         Obo                           EMBRACE Data and Methods ontology (data)
    edam_format       Obo                           EMBRACE Data and Methods ontology (formats)
    edam_identifier   Obo                           EMBRACE Data and Methods ontology (identifiers)
    edam_operation    Obo                           EMBRACE Data and Methods ontology (operations)
    edam_topic        Obo                           EMBRACE Data and Methods ontology (topics)
    go                Obo                           Gene Ontology
    go_component      Obo                           Gene Ontology (cellular components)
    go_function       Obo                           Gene Ontology (molecular functions)
    go_process        Obo                           Gene Ontology (biological processes)
    pw                Obo                           Pathways ontology
    ro                Obo                           Relations ontology
    so                Obo                           Sequence ontology
    swo               Obo                           Software ontology

Example 6

Display the information with no headings:

    % showdb -noheading
    Display information on configured databases

    bpsw              Protein,Protfeatures          BioPerl OBDA index of test SwissProt
    bpworm            Protein                       BioPerl OBDA index of test wormpep fasta file
    qapblast          Protein                       BLAST swissnew
    qapblastall       Protein                       BLAST swissnew, all fields indexed
    qapblastsplit     Protein                       BLAST swissnew split in 5 files
    qapblastsplitexc  Protein                       BLAST swissnew split in 5 files, not file 02
    qapblastsplitinc  Protein                       BLAST swissnew split in 5 files, only file 02
    qapfasta          Protein                       FASTA file swissnew entries
    qapflat           Protein,Protfeatures          SpTrEmbl flatfile
    qapflatall        Protein,Protfeatures          SpTrEmbl flatfiles, all fields indexed
    qapir             Protein,Protfeatures          Test PIR indexed by dbigcg
    qapirall          Protein,Protfeatures          Test PIR indexed by dbigcg with fields
    qapirexc          Protein,Protfeatures          Test PIR indexed by dbigcg except file pir1
    qapirinc          Protein,Protfeatures          Test PIR indexed by dbigcg file pir1
    qapxfasta         Protein                       FASTA file swissnew entries
    qapxflat          Protein                       Swissnew flatfiles
    qasrswww          Protein,Protfeatures          Remote SRS web server
    qaxpir            Protein,Protfeatures          PIR indexed by dbxgcg
    qaxpirall         Protein,Protfeatures          Test PIR indexed by dbxgcg with fields
    qaxpirexc         Protein,Protfeatures          Test PIR indexed by dbxgcg except pir1
    qaxpirinc         Protein,Protfeatures          Test PIR indexed by dbxgcg file pir1
    tpir              Protein                       Test PIR using NBRF access for 4 files
    tsw               Protein,Protfeatures,Text     Swissprot native format with EMBL CD-ROM index
    tswnew            Protein,Protfeatures          SpTrEmbl as 3 files in native format with EMBL CD-ROM index
    bpembl            Nucleotide,Nucfeatures        BioPerl OBDA index of test EMBL
    bpgb              Nucleotide,Nucfeatures        BioPerl OBDA index of test GenBank
    ena               Nucleotide,Nucfeatures        ENA via URL
    qanfasta          Nucleotide                    FASTA file EMBL rodents
    qanfastaall       Nucleotide                    FASTA file EMBL rodents, all fields indexed
    qanflat           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanflatall        Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanflatexc        Nucleotide,Nucfeatures        EMBL flatfiles, no rodent file
    qanflatinc        Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
    qangcg            Nucleotide,Nucfeatures        GCG format test EMBL
    qangcgall         Nucleotide,Nucfeatures        GCG format test EMBL
    qangcgexc         Nucleotide,Nucfeatures        GCG format test EMBL without prokaryotes
    qangcginc         Nucleotide,Nucfeatures        GCG format test EMBL only prokaryotes
    qanxfasta         Nucleotide                    FASTA file EMBL rodents
    qanxfastaall      Nucleotide                    FASTA file EMBL rodents, all fields indexed
    qanxflat          Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanxflatall       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields indexed
    qanxflatexc       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file
    qanxflatinc       Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
    qanxgcg           Nucleotide,Nucfeatures        GCG format EMBL
    qanxgcgall        Nucleotide,Nucfeatures        GCG format EMBL indexed by dbxgcg with query fields
    qanxgcgexc        Nucleotide,Nucfeatures        GCG format EMBL without prokaryotes
    qanxgcginc        Nucleotide,Nucfeatures        GCG format EMBL only prokaryotes
    qawfasta          Nucleotide                    FASTA file wormpep entries
    qawxfasta         Nucleotide                    FASTA file wormpep entries
    qaxembl           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    tembl             Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL CD-ROM index
    temblall          Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index
    temblrest         Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index
    temblvrt          Nucleotide,Nucfeatures        EMBL in native format with EMBL CD-ROM index
    tensembldasgrch37 Nucleotide                    Homo_sapiens Reference server based on GRCh37 assembly
    testdb            Nucleotide                    test sequence data
    tgb               Nucleotide,Nucfeatures        Genbank by SRS at DKFZ
    tgenbank          Nucleotide,Nucfeatures        Test GenBank in native format with EMBL CD-ROM index
    tgenedashuman     Nucleotide                    The Ensembl human Gene_ID reference source
    tflybase          Features                      Flybase CHADO server
    tgenedb           Features                      GeneDb CHADO server
    ttax              Taxonomy                      NCBI taxonomy test data
    taxon             Taxonomy                      NCBI taxonomy
    drcat             Resource                      Data Resource Catalogue
    tedam             Obo                           Test EDAM using dbxedam test indexes
    tobo              Obo                           Test EDAM using dbxobo test indexes
    chebi             Obo                           Chemical Entities of Biological Interest
    eco               Obo                           Evidence code ontology
    edam              Obo                           EMBRACE Data and Methods ontology
    edam_data         Obo                           EMBRACE Data and Methods ontology (data)
    edam_format       Obo                           EMBRACE Data and Methods ontology (formats)
    edam_identifier   Obo                           EMBRACE Data and Methods ontology (identifiers)
    edam_operation    Obo                           EMBRACE Data and Methods ontology (operations)
    edam_topic        Obo                           EMBRACE Data and Methods ontology (topics)
    go                Obo                           Gene Ontology
    go_component      Obo                           Gene Ontology (cellular components)
    go_function       Obo                           Gene Ontology (molecular functions)
    go_process        Obo                           Gene Ontology (biological processes)
    pw                Obo                           Pathways ontology
    ro                Obo                           Relations ontology
    so                Obo                           Sequence ontology
    swo               Obo                           Software ontology

Example 7

Display just a list of the available database names:

    % showdb -noheading -notype -noid -noquery -noall -nocomment -auto

    bpsw
    bpworm
    qapblast
    qapblastall
    qapblastsplit
    qapblastsplitexc
    qapblastsplitinc
    qapfasta
    qapflat
    qapflatall
    qapir
    qapirall
    qapirexc
    qapirinc
    qapxfasta
    qapxflat
    qasrswww
    qaxpir
    qaxpirall
    qaxpirexc
    qaxpirinc
    tpir
    tsw
    tswnew
    bpembl
    bpgb
    ena
    qanfasta
    qanfastaall
    qanflat
    qanflatall
    qanflatexc
    qanflatinc
    qangcg
    qangcgall
    qangcgexc
    qangcginc
    qanxfasta
    qanxfastaall
    qanxflat
    qanxflatall
    qanxflatexc
    qanxflatinc
    qanxgcg
    qanxgcgall
    qanxgcgexc
    qanxgcginc
    qawfasta
    qawxfasta
    qaxembl
    tembl
    temblall
    temblrest
    temblvrt
    tensembldasgrch37
    testdb
    tgb
    tgenbank
    tgenedashuman
    tflybase
    tgenedb
    ttax
    taxon
    drcat
    tedam
    tobo
    chebi
    eco
    edam
    edam_data
    edam_format
    edam_identifier
    edam_operation
    edam_topic
    go
    go_component
    go_function
    go_process
    pw
    ro
    so
    swo

Example 8

Display only the names and types:

    % showdb -only -type
    Display information on configured databases

    bpsw              Protein,Protfeatures
    bpworm            Protein
    qapblast          Protein
    qapblastall       Protein
    qapblastsplit     Protein
    qapblastsplitexc  Protein
    qapblastsplitinc  Protein
    qapfasta          Protein
    qapflat           Protein,Protfeatures
    qapflatall        Protein,Protfeatures
    qapir             Protein,Protfeatures
    qapirall          Protein,Protfeatures
    qapirexc          Protein,Protfeatures
    qapirinc          Protein,Protfeatures
    qapxfasta         Protein
    qapxflat          Protein
    qasrswww          Protein,Protfeatures
    qaxpir            Protein,Protfeatures
    qaxpirall         Protein,Protfeatures
    qaxpirexc         Protein,Protfeatures
    qaxpirinc         Protein,Protfeatures
    tpir              Protein
    tsw               Protein,Protfeatures,Text
    tswnew            Protein,Protfeatures
    bpembl            Nucleotide,Nucfeatures
    bpgb              Nucleotide,Nucfeatures
    ena               Nucleotide,Nucfeatures
    qanfasta          Nucleotide
    qanfastaall       Nucleotide
    qanflat           Nucleotide,Nucfeatures,Refseq
    qanflatall        Nucleotide,Nucfeatures,Refseq
    qanflatexc        Nucleotide,Nucfeatures
    qanflatinc        Nucleotide,Nucfeatures
    qangcg            Nucleotide,Nucfeatures
    qangcgall         Nucleotide,Nucfeatures
    qangcgexc         Nucleotide,Nucfeatures
    qangcginc         Nucleotide,Nucfeatures
    qanxfasta         Nucleotide
    qanxfastaall      Nucleotide
    qanxflat          Nucleotide,Nucfeatures,Refseq
    qanxflatall       Nucleotide,Nucfeatures,Refseq
    qanxflatexc       Nucleotide,Nucfeatures,Refseq
    qanxflatinc       Nucleotide,Nucfeatures
    qanxgcg           Nucleotide,Nucfeatures
    qanxgcgall        Nucleotide,Nucfeatures
    qanxgcgexc        Nucleotide,Nucfeatures
    qanxgcginc        Nucleotide,Nucfeatures
    qawfasta          Nucleotide
    qawxfasta         Nucleotide
    qaxembl           Nucleotide,Nucfeatures,Refseq
    tembl             Nucleotide,Refseq,Nucfeatures
    temblall          Nucleotide,Nucfeatures,Refseq
    temblrest         Nucleotide,Nucfeatures,Refseq
    temblvrt          Nucleotide,Nucfeatures
    tensembldasgrch37 Nucleotide
    testdb            Nucleotide
    tgb               Nucleotide,Nucfeatures
    tgenbank          Nucleotide,Nucfeatures
    tgenedashuman     Nucleotide
    tflybase          Features
    tgenedb           Features
    ttax              Taxonomy
    taxon             Taxonomy
    drcat             Resource
    tedam             Obo
    tobo              Obo
    chebi             Obo
    eco               Obo
    edam              Obo
    edam_data         Obo
    edam_format       Obo
    edam_identifier   Obo
    edam_operation    Obo
    edam_topic        Obo
    go                Obo
    go_component      Obo
    go_function       Obo
    go_process        Obo
    pw                Obo
    ro                Obo
    so                Obo
    swo               Obo

Example 9

Display everything

    % showdb -full
    Display information on configured databases

    # Name            Type                          ID  Qry All Method    Taxon                       Fields                                                                                                Aliases         Examples           Defined  Release             Comment
    # =============== ============================= ==  === === ========= =========================== ===================================================================================================== =============== ================== ======== =================== =======
    bpsw              Protein,Protfeatures          OK  OK  OK  obda      -                                2 id,acc                                                                                               0 -              0 -         special                      BioPerl OBDA index of test SwissProt
    bpworm            Protein                       OK  OK  OK  obda      -                                1 id                                                                                                   0 -              0 -         special                      BioPerl OBDA index of test wormpep fasta file
    qapblast          Protein                       OK  OK  OK  blast     1_all                            2 id,acc                                                                                               0 -              0 -         special                      BLAST swissnew
    qapblastall       Protein                       OK  OK  OK  blast     1_all                            4 sv,des                                                                                               0 -              0 -         special                      BLAST swissnew, all fields indexed
    qapblastsplit     Protein                       OK  OK  OK  blast     1_all                            2 id,acc                                                                                               0 -              0 -         special                      BLAST swissnew split in 5 files
    qapblastsplitexc  Protein                       OK  OK  OK  blast     1_all                            2 id,acc                                                                                               0 -              0 -         special                      BLAST swissnew split in 5 files, not file 02
    qapblastsplitinc  Protein                       OK  OK  OK  blast     1_all                            2 id,acc                                                                                               0 -              0 -         special                      BLAST swissnew split in 5 files, only file 02
    qapfasta          Protein                       OK  OK  OK  emblcd    1_all                            2 id,acc                                                                                               0 -              0 -         special                      FASTA file swissnew entries
    qapflat           Protein,Protfeatures          OK  OK  OK  emblcd    1_all                            2 id,acc                                                                                               0 -              0 -         special                      SpTrEmbl flatfile
    qapflatall        Protein,Protfeatures          OK  OK  OK  emblcd    1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special                      SpTrEmbl flatfiles, all fields indexed
    qapir             Protein,Protfeatures          OK  OK  OK  gcg       1_all                            2 id,acc                                                                                               0 -              0 -         special                      Test PIR indexed by dbigcg
    qapirall          Protein,Protfeatures          OK  OK  OK  gcg       1_all                            5 des,org,key                                                                                          0 -              0 -         special                      Test PIR indexed by dbigcg with fields
    qapirexc          Protein,Protfeatures          OK  OK  OK  gcg       1_all                            2 id,acc                                                                                               0 -              0 -         special                      Test PIR indexed by dbigcg except file pir1
    qapirinc          Protein,Protfeatures          OK  OK  OK  gcg       1_all                            2 id,acc                                                                                               0 -              0 -         special                      Test PIR indexed by dbigcg file pir1
    qapxfasta         Protein                       OK  OK  OK  emboss    1_all                            2 id,acc                                                                                               0 -              0 -         special                      FASTA file swissnew entries
    qapxflat          Protein                       OK  OK  OK  emboss    1_all                            2 id,acc                                                                                               0 -              0 -         special                      Swissnew flatfiles
    qasrswww          Protein,Protfeatures          OK  OK  OK  srswww    1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special                      Remote SRS web server
    qaxpir            Protein,Protfeatures          OK  OK  OK  embossgcg 1_all                            2 id,acc                                                                                               0 -              0 -         special                      PIR indexed by dbxgcg
    qaxpirall         Protein,Protfeatures          OK  OK  OK  embossgcg 1_all                            5 des,org,key                                                                                          0 -              0 -         special                      Test PIR indexed by dbxgcg with fields
    qaxpirexc         Protein,Protfeatures          OK  OK  OK  embossgcg 1_all                            2 id,acc                                                                                               0 -              0 -         special                      Test PIR indexed by dbxgcg except pir1
    qaxpirinc         Protein,Protfeatures          OK  OK  OK  embossgcg 1_all                            2 id,acc                                                                                               0 -              0 -         special                      Test PIR indexed by dbxgcg file pir1
    tpir              Protein                       OK  OK  OK  gcg       1_all                            5 des,org,key                                                                                          0 -              0 -         special                      Test PIR using NBRF access for 4 files
    tsw               Protein,Protfeatures,Text     OK  OK  OK  emblcd    1_all                            6 id,acc,sv,des,org,key                                                                                0 -              1 hba_human special  36                  Swissprot native format with EMBL CD-ROM index
    tswnew            Protein,Protfeatures          OK  OK  OK  emblcd    1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special  37                  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
    bpembl            Nucleotide,Nucfeatures        OK  OK  OK  obda      -                                2 id,acc                                                                                               0 -              0 -         special                      BioPerl OBDA index of test EMBL
    bpgb              Nucleotide,Nucfeatures        OK  OK  OK  obda      -                                2 id,acc                                                                                               0 -              0 -         special                      BioPerl OBDA index of test GenBank
    ena               Nucleotide,Nucfeatures        OK  OK  OK  url       1_all                            2 id,acc                                                                                               0 -              0 -         special                      ENA via URL
    qanfasta          Nucleotide                    OK  OK  OK  emblcd    9989_rodentia                    2 id,acc                                                                                               0 -              0 -         special                      FASTA file EMBL rodents
    qanfastaall       Nucleotide                    OK  OK  OK  emblcd    9989_rodentia                    4 sv,des                                                                                               0 -              0 -         special                      FASTA file EMBL rodents, all fields indexed
    qanflat           Nucleotide,Nucfeatures,Refseq OK  OK  OK  emblcd    1_all                            2 id,acc                                                                                               0 -              0 -         special                      EMBL flatfiles
    qanflatall        Nucleotide,Nucfeatures,Refseq OK  OK  OK  emblcd    1_all                            2 id,acc                                                                                               0 -              0 -         special                      EMBL flatfiles
    qanflatexc        Nucleotide,Nucfeatures        OK  OK  OK  emblcd    1_all                            2 id,acc                                                                                               0 -              0 -         special                      EMBL flatfiles, no rodent file
    qanflatinc        Nucleotide,Nucfeatures        OK  OK  OK  emblcd    -                                2 id,acc                                                                                               0 -              0 -         special                      EMBL flatfiles, only rodent file
    qangcg            Nucleotide,Nucfeatures        OK  OK  OK  gcg       1_all                            2 id,acc                                                                                               0 -              0 -         special                      GCG format test EMBL
    qangcgall         Nucleotide,Nucfeatures        OK  OK  OK  gcg       1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special                      GCG format test EMBL
    qangcgexc         Nucleotide,Nucfeatures        OK  OK  OK  gcg       1_all                            2 id,acc                                                                                               0 -              0 -         special                      GCG format test EMBL without prokaryotes
    qangcginc         Nucleotide,Nucfeatures        OK  OK  OK  gcg       1_all                            2 id,acc                                                                                               0 -              0 -         special                      GCG format test EMBL only prokaryotes
    qanxfasta         Nucleotide                    OK  OK  OK  emboss    9989_rodentia                    2 id,acc                                                                                               0 -              0 -         special                      FASTA file EMBL rodents
    qanxfastaall      Nucleotide                    OK  OK  OK  emboss    9989_rodentia                    4 sv,des                                                                                               0 -              0 -         special                      FASTA file EMBL rodents, all fields indexed
    qanxflat          Nucleotide,Nucfeatures,Refseq OK  OK  OK  emboss    1_all                            2 id,acc                                                                                               0 -              0 -         special                      EMBL flatfiles
    qanxflatall       Nucleotide,Nucfeatures,Refseq OK  OK  OK  emboss    1_all                            6 des,org,key,sv                                                                                       0 -              0 -         special                      EMBL flatfiles, all fields indexed
    qanxflatexc       Nucleotide,Nucfeatures,Refseq OK  OK  OK  emboss    1_all                            2 id,acc                                                                                               0 -              0 -         special                      EMBL flatfiles, no rodent file
    qanxflatinc       Nucleotide,Nucfeatures        OK  OK  OK  emboss    1_all                            2 id,acc                                                                                               0 -              0 -         special                      EMBL flatfiles, only rodent file
    qanxgcg           Nucleotide,Nucfeatures        OK  OK  OK  embossgcg 1_all                            2 id,acc                                                                                               0 -              0 -         special                      GCG format EMBL
    qanxgcgall        Nucleotide,Nucfeatures        OK  OK  OK  embossgcg 1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special                      GCG format EMBL indexed by dbxgcg with query fields
    qanxgcgexc        Nucleotide,Nucfeatures        OK  OK  OK  embossgcg 1_all                            2 id,acc                                                                                               0 -              0 -         special                      GCG format EMBL without prokaryotes
    qanxgcginc        Nucleotide,Nucfeatures        OK  OK  OK  embossgcg 1_all                            2 id,acc                                                                                               0 -              0 -         special                      GCG format EMBL only prokaryotes
    qawfasta          Nucleotide                    OK  OK  OK  emblcd    6239_caenorhabditis_elegans      2 id,acc                                                                                               0 -              0 -         special                      FASTA file wormpep entries
    qawxfasta         Nucleotide                    OK  OK  OK  emboss    6239_caenorhabditis_elegans      2 id,acc                                                                                               0 -              0 -         special                      FASTA file wormpep entries
    qaxembl           Nucleotide,Nucfeatures,Refseq OK  OK  OK  emboss    1_all                            2 id,acc                                                                                               0 -              0 -         special                      EMBL flatfiles
    tembl             Nucleotide,Refseq,Nucfeatures OK  OK  OK  emblcd    1_all                            6 sv,des,org,key                                                                                       0 -              1 x13776    special  57                  EMBL in native format with EMBL CD-ROM index
    temblall          Nucleotide,Nucfeatures,Refseq OK  OK  OK  direct    1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special  57                  EMBL in native format with EMBL CD-ROM index
    temblrest         Nucleotide,Nucfeatures,Refseq OK  OK  OK  direct    1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special  57                  EMBL in native format with EMBL CD-ROM index
    temblvrt          Nucleotide,Nucfeatures        OK  OK  OK  direct    9711_chordata                    6 sv,des,org,key                                                                                       0 -              0 -         special  57                  EMBL in native format with EMBL CD-ROM index
    tensembldasgrch37 Nucleotide                    OK  OK  -   das       9606_homo_sapiens                2 id,acc                                                                                               0 -              0 -         special                      Homo_sapiens Reference server based on GRCh37 assembly
    testdb            Nucleotide                    OK  OK  OK  emblcd    -                                3 des                                                                                                  0 -              0 -         special  01                  test sequence data
    tgb               Nucleotide,Nucfeatures        OK  OK  OK  srswww    1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special                      Genbank by SRS at DKFZ
    tgenbank          Nucleotide,Nucfeatures        OK  OK  OK  emblcd    1_all                            6 sv,des,org,key                                                                                       0 -              0 -         special  01                  Test GenBank in native format with EMBL CD-ROM index
    tgenedashuman     Nucleotide                    OK  OK  -   das       9606_homo_sapiens                2 id,acc                                                                                               0 -              0 -         special                      The Ensembl human Gene_ID reference source
    tflybase          Features                      OK  -   -   chado(id) 1_all                            2 uniquename                                                                                           0 -              0 -         special                      Flybase CHADO server
    tgenedb           Features                      OK  -   -   chado(id) 1_all                            2 uniquename                                                                                           0 -              0 -         special                      GeneDb CHADO server
    ttax              Taxonomy                      OK  OK  OK  embosstax -                                7 id,acc,nam,rnk,up,gc,mgc                                                                             0 -              0 -         special                      NCBI taxonomy test data
    taxon             Taxonomy                      OK  OK  OK  embosstax 1                                7 id,acc,tax,rnk,up,gc,mgc                                                                             0 -              0 -         standard July 2012           NCBI taxonomy
    drcat             Resource                      OK  OK  OK  emboss    none                            21 id,acc,nam,des,url,cat,edat,efmt,eid,etpc,xref,qout,qfmt,qin,qurl,cc,rest,soap,stat,xref,taxid       0 -              0 -         standard alpha 1 21-jun-2011 Data Resource Catalogue
    tedam             Obo                           OK  OK  OK  emboss    -                               12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                          0 -              0 -         special  beta11              Test EDAM using dbxedam test indexes
    tobo              Obo                           OK  OK  OK  emboss    -                               12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                          0 -              0 -         special  beta11              Test EDAM using dbxobo test indexes
    chebi             Obo                           OK  OK  OK  emboss    none                             5 id,acc,nam,isa,des                                                                                   0 -              0 -         standard 93                  Chemical Entities of Biological Interest
    eco               Obo                           OK  OK  OK  emboss    none                             5 id,acc,nam,isa,des                                                                                   0 -              0 -         standard 2.02                Evidence code ontology
    edam              Obo                           OK  OK  OK  emboss    none                            12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                          0 -              0 -         standard 1.1                 EMBRACE Data and Methods ontology
    edam_data         Obo                           OK  OK  OK  emboss    none                            12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                          0 -              0 -         standard 1.1                 EMBRACE Data and Methods ontology (data)
    edam_format       Obo                           OK  OK  OK  emboss    none                            12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                          0 -              0 -         standard 1.1                 EMBRACE Data and Methods ontology (formats)
    edam_identifier   Obo                           OK  OK  OK  emboss    none                            12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                          0 -              0 -         standard 1.1                 EMBRACE Data and Methods ontology (identifiers)
    edam_operation    Obo                           OK  OK  OK  emboss    none                            12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                          0 -              0 -         standard 1.1                 EMBRACE Data and Methods ontology (operations)
    edam_topic        Obo                           OK  OK  OK  emboss    none                            12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                          0 -              0 -         standard 1.1                 EMBRACE Data and Methods ontology (topics)
    go                Obo                           OK  OK  OK  emboss    1_all                            6 id,acc,nam,isa,des,ns                                                                                0 -              0 -         standard 1.1.3300            Gene Ontology
    go_component      Obo                           OK  OK  OK  emboss    1_all                            6 id,acc,nam,isa,des,ns                                                                                0 -              0 -         standard 1.1.3300            Gene Ontology (cellular components)
    go_function       Obo                           OK  OK  OK  emboss    1_all                            6 id,acc,nam,isa,des,ns                                                                                0 -              0 -         standard 1.1.3300            Gene Ontology (molecular functions)
    go_process        Obo                           OK  OK  OK  emboss    1_all                            6 id,acc,nam,isa,des,ns                                                                                0 -              0 -         standard 1.1.3300            Gene Ontology (biological processes)
    pw                Obo                           OK  OK  OK  emboss    1_all                            5 id,acc,nam,isa,des                                                                                   0 -              0 -         standard 12:06:2012 11:03    Pathways ontology
    ro                Obo                           OK  OK  OK  emboss    none                             5 id,acc,nam,isa,des                                                                                   0 -              0 -         standard 20:03:2009 11:58    Relations ontology
    so                Obo                           OK  OK  OK  emboss    none                             5 id,acc,nam,isa,des                                                                                   0 -              0 -         standard 02:05:2012 11:08    Sequence ontology
    swo               Obo                           OK  OK  OK  emboss    none                             5 id,acc,nam,isa,des                                                                                   0 -              0 -         standard 12-jul-2012         Software ontology

## Command line arguments

    Display information on configured databases
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers: (none)
       Additional (Optional) qualifiers:
       -database           string     Name of a single database to give
                                      information on (Any string)
       -html               boolean    [N] Format output as an HTML table
       -[no]protein        boolean    [Y] Display protein databases
       -[no]nucleic        boolean    [Y] Display nucleotide databases
       -[no]sequence       boolean    [Y] Display general sequence databases
       -[no]feature        boolean    [Y] Display feature annotation databases
       -[no]text           boolean    [Y] Display text databases
       -[no]taxonomy       boolean    [Y] Display taxonomy databases
       -[no]resource       boolean    [Y] Display resource databases
       -[no]assembly       boolean    [Y] Display sequence assembly databases
       -[no]obo            boolean    [Y] Display obo bio-ontology databases
       -[no]xml            boolean    [Y] Display XML databases
       -[no]standard       boolean    [Y] Display standard databases
       -[no]user           boolean    [Y] Display user-defined databases
       -[no]include        boolean    [Y] Display databases defined in included
                                      files
       -full               boolean    [N] Display all columns
       -access             boolean    [$(full)] This displays the levels of access
                                      that can be used on this database
       -methods            boolean    [$(full)] This displays the access methods
                                      that can be used on this database, for all,
                                      query or ID access
       -taxscope           boolean    [$(full)] This displays the taxons covered
                                      by this database
       -fields             boolean    [$(full)] This displays the search fields
                                      that can be used on this database, including
                                      the standard 'id' or 'acc' fields
       -numfields          boolean    [$(full)] This displays the number of search
                                      fields that can be used on this database,
                                      including the standard 'id' or 'acc' fields
       -aliases            boolean    [$(full)] This displays the alias names that
                                      can be used for this database
       -numaliases         boolean    [$(full)] This displays the number of alias
                                      names that can be used for this database
       -examples           boolean    [$(full)] This displays the example queries
                                      that can be used to test this database
       -numexamples        boolean    [$(full)] This displays the number of
                                      example queries that can be used to test
                                      this database
       -defined            boolean    [$(full)] This displays a short name for the
                                      file containing the database definition
       -release            boolean    [$(full)] Display 'release' column
       -outfile            outfile    [stdout] Output file name

       Advanced (Unprompted) qualifiers:
       -only               toggle     [N] This is a way of shortening the command
                                      line if you only want a few standard columns
                                      to be displayed. Instead of specifying:
                                      '-nohead -notype -noid -noquery -noall'
                                      to get only the comment output, you can
                                      specify
                                      '-only -comment'
       -heading            boolean    [@(!$(only))] Display column headings
       -type               boolean    [@(!$(only))] Display 'type' column
       -id                 boolean    [@(!$(only))] Display 'id' access column
       -query              boolean    [@(!$(only))] Display 'qry' access column
       -all                boolean    [@(!$(only))] Display 'all' access column
       -comment            boolean    [@(!$(only))] Display 'comment' column

       Associated qualifiers:

       "-outfile" associated qualifiers
       -odirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
(none)
Additional (Optional) qualifiers
-database | string | Name of a single database to give information on | Any string |
-html | boolean | Format output as an HTML table | Boolean value Yes/No | No
-[no]protein | boolean | Display protein databases | Boolean value Yes/No | Yes
-[no]nucleic | boolean | Display nucleotide databases | Boolean value Yes/No | Yes
-[no]sequence | boolean | Display general sequence databases | Boolean value Yes/No | Yes
-[no]feature | boolean | Display feature annotation databases | Boolean value Yes/No | Yes
-[no]text | boolean | Display text databases | Boolean value Yes/No | Yes
-[no]taxonomy | boolean | Display taxonomy databases | Boolean value Yes/No | Yes
-[no]resource | boolean | Display resource databases | Boolean value Yes/No | Yes
-[no]assembly | boolean | Display sequence assembly databases | Boolean value Yes/No | Yes
-[no]obo | boolean | Display obo bio-ontology databases | Boolean value Yes/No | Yes
-[no]xml | boolean | Display XML databases | Boolean value Yes/No | Yes
-[no]standard | boolean | Display standard databases | Boolean value Yes/No | Yes
-[no]user | boolean | Display user-defined databases | Boolean value Yes/No | Yes
-[no]include | boolean | Display databases defined in included files | Boolean value Yes/No | Yes
-full | boolean | Display all columns | Boolean value Yes/No | No
-access | boolean | This displays the levels of access that can be used on this database | Boolean value Yes/No | $(full)
-methods | boolean | This displays the access methods that can be used on this database, for all, query or ID access | Boolean value Yes/No | $(full)
-taxscope | boolean | This displays the taxons covered by this database | Boolean value Yes/No | $(full)
-fields | boolean | This displays the search fields that can be used on this database, including the standard 'id' or 'acc' fields | Boolean value Yes/No | $(full)
-numfields | boolean | This displays the number of search fields that can be used on this database, including the standard 'id' or 'acc' fields | Boolean value Yes/No | $(full)
-aliases | boolean | This displays the alias names that can be used for this database | Boolean value Yes/No | $(full)
-numaliases | boolean | This displays the number of alias names that can be used for this database | Boolean value Yes/No | $(full)
-examples | boolean | This displays the example queries that can be used to test this database | Boolean value Yes/No | $(full)
-numexamples | boolean | This displays the number of example queries that can be used to test this database | Boolean value Yes/No | $(full)
-defined | boolean | This displays a short name for the file containing the database definition | Boolean value Yes/No | $(full)
-release | boolean | Display 'release' column | Boolean value Yes/No | $(full)
-outfile | outfile | Output file name | Output file | stdout
Advanced (Unprompted) qualifiers
-only | toggle | This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' | Toggle value Yes/No | No
-heading | boolean | Display column headings | Boolean value Yes/No | @(!$(only))
-type | boolean | Display 'type' column | Boolean value Yes/No | @(!$(only))
-id | boolean | Display 'id' access column | Boolean value Yes/No | @(!$(only))
-query | boolean | Display 'qry' access column | Boolean value Yes/No | @(!$(only))
-all | boolean | Display 'all' access column | Boolean value Yes/No | @(!$(only))
-comment | boolean | Display 'comment' column | Boolean value Yes/No | @(!$(only))
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

showdb examines the databases defined for this EMBOSS installation and for the current user.

### Input files for usage example 3

'tsw' is a sequence entry in the example protein database 'tsw'

## Output file format

### Output files for usage example 2

### File: showdb.out

    # Name            Type                          Comment
    # =============== ============================= =======
    bpsw              Protein,Protfeatures          BioPerl OBDA index of test SwissProt
    bpworm            Protein                       BioPerl OBDA index of test wormpep fasta file
    qapblast          Protein                       BLAST swissnew
    qapblastall       Protein                       BLAST swissnew, all fields indexed
    qapblastsplit     Protein                       BLAST swissnew split in 5 files
    qapblastsplitexc  Protein                       BLAST swissnew split in 5 files, not file 02
    qapblastsplitinc  Protein                       BLAST swissnew split in 5 files, only file 02
    qapfasta          Protein                       FASTA file swissnew entries
    qapflat           Protein,Protfeatures          SpTrEmbl flatfile
    qapflatall        Protein,Protfeatures          SpTrEmbl flatfiles, all fields indexed
    qapir             Protein,Protfeatures          Test PIR indexed by dbigcg
    qapirall          Protein,Protfeatures          Test PIR indexed by dbigcg with fields
    qapirexc          Protein,Protfeatures          Test PIR indexed by dbigcg except file pir1
    qapirinc          Protein,Protfeatures          Test PIR indexed by dbigcg file pir1
    qapxfasta         Protein                       FASTA file swissnew entries
    qapxflat          Protein                       Swissnew flatfiles
    qasrswww          Protein,Protfeatures          Remote SRS web server
    qaxpir            Protein,Protfeatures          PIR indexed by dbxgcg
    qaxpirall         Protein,Protfeatures          Test PIR indexed by dbxgcg with fields
    qaxpirexc         Protein,Protfeatures          Test PIR indexed by dbxgcg except pir1
    qaxpirinc         Protein,Protfeatures          Test PIR indexed by dbxgcg file pir1
    tpir              Protein                       Test PIR using NBRF access for 4 files
    tsw               Protein,Protfeatures,Text     Swissprot native format with EMBL CD-ROM index
    tswnew            Protein,Protfeatures          SpTrEmbl as 3 files in native format with EMBL CD-ROM index
    bpembl            Nucleotide,Nucfeatures        BioPerl OBDA index of test EMBL
    bpgb              Nucleotide,Nucfeatures        BioPerl OBDA index of test GenBank
    ena               Nucleotide,Nucfeatures        ENA via URL
    qanfasta          Nucleotide                    FASTA file EMBL rodents
    qanfastaall       Nucleotide                    FASTA file EMBL rodents, all fields indexed
    qanflat           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanflatall        Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanflatexc        Nucleotide,Nucfeatures        EMBL flatfiles, no rodent file
    qanflatinc        Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
    qangcg            Nucleotide,Nucfeatures        GCG format test EMBL
    qangcgall         Nucleotide,Nucfeatures        GCG format test EMBL
    qangcgexc         Nucleotide,Nucfeatures        GCG format test EMBL without prokaryotes
    qangcginc         Nucleotide,Nucfeatures        GCG format test EMBL only prokaryotes
    qanxfasta         Nucleotide                    FASTA file EMBL rodents
    qanxfastaall      Nucleotide                    FASTA file EMBL rodents, all fields indexed
    qanxflat          Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    qanxflatall       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields indexed
    qanxflatexc       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file
    qanxflatinc       Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
    qanxgcg           Nucleotide,Nucfeatures        GCG format EMBL
    qanxgcgall        Nucleotide,Nucfeatures        GCG format EMBL indexed by dbxgcg with query fields
    qanxgcgexc        Nucleotide,Nucfeatures        GCG format EMBL without prokaryotes
    qanxgcginc        Nucleotide,Nucfeatures        GCG format EMBL only prokaryotes
    qawfasta          Nucleotide                    FASTA file wormpep entries
    qawxfasta         Nucleotide                    FASTA file wormpep entries
    qaxembl           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
    tembl             Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL CD-ROM index
    temblall          Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index
    temblrest         Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index
    temblvrt          Nucleotide,Nucfeatures        EMBL in native format with EMBL CD-ROM index
    tensembldasgrch37 Nucleotide                    Homo_sapiens Reference server based on GRCh37 assembly
    testdb            Nucleotide                    test sequence data
    tgb               Nucleotide,Nucfeatures        Genbank by SRS at DKFZ
    tgenbank          Nucleotide,Nucfeatures        Test GenBank in native format with EMBL CD-ROM index
    tgenedashuman     Nucleotide                    The Ensembl human Gene_ID reference source
    tflybase          Features                      Flybase CHADO server
    tgenedb           Features                      GeneDb CHADO server
    ttax              Taxonomy                      NCBI taxonomy test data
    taxon             Taxonomy                      NCBI taxonomy
    drcat             Resource                      Data Resource Catalogue
    tedam             Obo                           Test EDAM using dbxedam test indexes
    tobo              Obo                           Test EDAM using dbxobo test indexes
    chebi             Obo                           Chemical Entities of Biological Interest
    eco               Obo                           Evidence code ontology
    edam              Obo                           EMBRACE Data and Methods ontology
    edam_data         Obo                           EMBRACE Data and Methods ontology (data)
    edam_format       Obo                           EMBRACE Data and Methods ontology (formats)
    edam_identifier   Obo                           EMBRACE Data and Methods ontology (identifiers)
    edam_operation    Obo                           EMBRACE Data and Methods ontology (operations)
    edam_topic        Obo                           EMBRACE Data and Methods ontology (topics)
    go                Obo                           Gene Ontology
    go_component      Obo                           Gene Ontology (cellular components)
    go_function       Obo                           Gene Ontology (molecular functions)
    go_process        Obo                           Gene Ontology (biological processes)
    pw                Obo                           Pathways ontology
    ro                Obo                           Relations ontology
    so                Obo                           Sequence ontology
    swo               Obo                           Software ontology

The output is a simple text table.

Type 'P' indicates that this is a Protein database.

Type 'N' indicates that this is a Nucleic database.

'OK' under ID, Qry or All indicates that that access method can be used on this database. A '-' indicates that you cannot access this database in that way.

Note that 'OK' does not mean that the database is working correctly. It simply means that showdb has read the database definition correctly and that this method of access to the database should be possible.

If you are setting up a new database, then you should check that it works correctly by extracting entries from it using seqret.

When the -html qualifier is specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are not output by this program as the table of databases is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user.

## Data files

The databases are specified in the files "emboss.defaults" for site wide definitions, and "~/.embossrc" for the user's own settings.

## Notes

EMBOSS provides excellent database support. All the common sequence formats you are likely to come across are supported. There are three basic levels of database query with different ways to search for and retrieve entries: `entry` A single entry specified by database ID or accession number is retrieved. For example "embl:x13776". `query` One or more entries matching a wildcard string in the USA are retrieved (this can be slow for some methods). For example you can specify all of the human PAX proteins in SWISS_PROT by: `swissprot:pax*_human`. `all` All entries are read sequentially from a database. For example to specify all entries in the database use `embl:*`.

One or more query levels may be available for a database depending on the database in question and how it has been setup and indexed. Each database and access method must be configured for it to be available for use. This involves editing one of the EMBOSS configuration files, either your own personal `.embossrc` or the installation-wide `emboss.default` file. The `emboss.default` file will typically contain the definitions of the test databases (`tsw`, `tembl`, `tpir`, etc) used in the usage examples for the application documentation and serve as example database definitions. For more information, see the EMBOSS Administrators Manual. You can run showdb to see the databases and access methods that have been configured successfully.

## References

None.

## Warnings

Where the string `OK` is given next to a database is listed in showdb output, this means showdb has read the database definition correctly and that this access method is in principle possible, in other words, the database has been configured correctly.. It does not mean that the database or access method are available or working correctly. You should check things are ok by running, for example, seqret to retrieve an entry.

## Diagnostic Error Messages

"The database 'xyz' does not exist" You have supplied the name of a database with the -database qualifier, but that database does not exist as far as EMBOSS is concerned.

## Exit status

It always exits with status 0, unless the above diagnostic message is displayed.

## Known bugs

None noted.

## See also

Program name | Description
--- | ---
cachedas | Generate server cache file for DAS servers or for the DAS registry
cachedbfetch | Generate server cache file for Dbfetch/WSDbfetch data sources
cacheebeyesearch | Generate server cache file for EB-eye search domains
cacheensembl | Generate server cache file for an Ensembl server
dbtell | Display information about a public database
servertell | Display information about a public server
showserver | Display information on configured servers

## Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

Completed 6th August 1999.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None