                                   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       ID  Qry All Comment
# =============== ========== ==  === === =======
bpsw              Protein    OK  OK  OK
bpworm            Protein    OK  OK  OK
qapblast          Protein    OK  OK  OK  BLAST swissnew
qapblastall       Protein    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, not fi
le 02
qapblastsplitinc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, only f
ile 02
qapfasta          Protein    OK  OK  OK  FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  PIR
qapirall          Protein    OK  OK  OK  PIR
qapirexc          Protein    OK  OK  OK  PIR
qapirinc          Protein    OK  OK  OK  PIR
qapxfasta         Protein    OK  OK  OK  FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  PIR
qaxpirall         Protein    OK  OK  OK  PIR
qaxpirexc         Protein    OK  OK  OK  PIR
qaxpirinc         Protein    OK  OK  OK  PIR
tpir              Protein    OK  OK  OK  PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  Swissprot native format with EMBL CD-RO
M index
tswnew            Protein    OK  OK  OK  SpTrEmbl as 3 files in native format wi
th EMBL CD-ROM index
bpembl            Nucleotide OK  OK  OK
bpgb              Nucleotide OK  OK  OK
qanfasta          Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall       Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields ind
exed
qanflat           Nucleotide OK  OK  OK  EMBL flatfiles
qanflatall        Nucleotide OK  OK  OK  EMBL flatfiles
qanflatexc        Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc        Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qangcg            Nucleotide OK  OK  OK  GCG format EMBL
qangcgall         Nucleotide OK  OK  OK  GCG format EMBL
qangcgexc         Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc         Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanxfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields ind
exed
qanxflat          Nucleotide OK  OK  OK  EMBL flatfiles
qanxflatall       Nucleotide OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg           Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgall        Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgexc        Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qasrswww          Nucleotide OK  OK  OK  Remote SRS web server
qawfasta          Nucleotide OK  OK  OK  FASTA file wormpep entries
qawxfasta         Nucleotide OK  OK  OK  FASTA file wormpep entries
qaxembl           Nucleotide OK  OK  OK  EMBL flatfiles
tembl             Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblall          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblrest         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblvrt          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
tensembldasgrch37 Nucleotide OK  -   -   Homo_sapiens Reference server based on
GRCh37 assembly
testdb            Nucleotide OK  OK  OK  test sequence data
tgb               Nucleotide OK  OK  OK  Genbank IDs
tgenbank          Nucleotide OK  OK  OK  GenBank in native format with EMBL CD-R
OM index
tgenedashuman     Nucleotide OK  -   -   The Ensembl human Gene_ID reference sou
rce
tflybase          Features   OK  -   -
tgenedb           Features   OK  -   -
ttax              Taxonomy   OK  OK  OK
taxon             Taxonomy   OK  OK  OK
drcat             Resource   OK  OK  OK
tedam             Obo        OK  OK  OK  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  EDAM using dbxobo test indexes
chebi             Obo        OK  OK  OK
eco               Obo        OK  OK  OK
edam              Obo        OK  OK  OK
edam_data         Obo        OK  OK  OK
edam_format       Obo        OK  OK  OK
edam_identifier   Obo        OK  OK  OK
edam_operation    Obo        OK  OK  OK
edam_topic        Obo        OK  OK  OK
go                Obo        OK  OK  OK
go_component      Obo        OK  OK  OK
go_function       Obo        OK  OK  OK
go_process        Obo        OK  OK  OK
pw                Obo        OK  OK  OK
ro                Obo        OK  OK  OK
so                Obo        OK  OK  OK
swo               Obo        OK  OK  OK


   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    ID  Qry All Comment
# ============ ======= ==  === === =======
tsw            Protein OK  OK  OK  Swissprot native format with EMBL CD-ROM inde
x


   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


 Name Type ID Qry All Comment

 bpsw Protein OK   OK   OK

 bpworm Protein OK   OK   OK

 qapblast Protein OK   OK   OK   BLAST swissnew

 qapblastall Protein OK   OK   OK   BLAST swissnew, all fields indexed

 qapblastsplit Protein OK   OK   OK   BLAST swissnew split in 5 files

 qapblastsplitexc Protein OK   OK   OK   BLAST swissnew split in 5 files, not fi
le 02

 qapblastsplitinc Protein OK   OK   OK   BLAST swissnew split in 5 files, only f
ile 02

 qapfasta Protein OK   OK   OK   FASTA file swissnew entries

 qapflat Protein OK   OK   OK   SpTrEmbl flatfile

 qapflatall Protein OK   OK   OK   SpTrEmbl flatfiles, all fields indexed

 qapir Protein OK   OK   OK   PIR

 qapirall Protein OK   OK   OK   PIR

 qapirexc Protein OK   OK   OK   PIR

 qapirinc Protein OK   OK   OK   PIR

 qapxfasta Protein OK   OK   OK   FASTA file swissnew entries

 qapxflat Protein OK   OK   OK   Swissnew flatfiles

 qaxpir Protein OK   OK   OK   PIR

 qaxpirall Protein OK   OK   OK   PIR

 qaxpirexc Protein OK   OK   OK   PIR

 qaxpirinc Protein OK   OK   OK   PIR

 tpir Protein OK   OK   OK   PIR using NBRF access for 4 files

 tsw Protein OK   OK   OK   Swissprot native format with EMBL CD-ROM index

 tswnew Protein OK   OK   OK   SpTrEmbl as 3 files in native format with EMBL CD
-ROM index

 bpembl Nucleotide OK   OK   OK

 bpgb Nucleotide OK   OK   OK

 qanfasta Nucleotide OK   OK   OK   FASTA file EMBL rodents

 qanfastaall Nucleotide OK   OK   OK   FASTA file EMBL rodents, all fields index
ed

 qanflat Nucleotide OK   OK   OK   EMBL flatfiles

 qanflatall Nucleotide OK   OK   OK   EMBL flatfiles

 qanflatexc Nucleotide OK   OK   OK   EMBL flatfiles, no rodent file

 qanflatinc Nucleotide OK   OK   OK   EMBL flatfiles, only rodent file

 qangcg Nucleotide OK   OK   OK   GCG format EMBL

 qangcgall Nucleotide OK   OK   OK   GCG format EMBL

 qangcgexc Nucleotide OK   OK   OK   GCG format EMBL without prokaryotes

 qangcginc Nucleotide OK   OK   OK   GCG format EMBL only prokaryotes

 qanxfasta Nucleotide OK   OK   OK   FASTA file EMBL rodents

 qanxfastaall Nucleotide OK   OK   OK   FASTA file EMBL rodents, all fields inde
xed

 qanxflat Nucleotide OK   OK   OK   EMBL flatfiles

 qanxflatall Nucleotide OK   OK   OK   EMBL flatfiles, all fields indexed

 qanxflatexc Nucleotide OK   OK   OK   EMBL flatfiles, no rodent file

 qanxflatinc Nucleotide OK   OK   OK   EMBL flatfiles, only rodent file

 qanxgcg Nucleotide OK   OK   OK   GCG format EMBL

 qanxgcgall Nucleotide OK   OK   OK   GCG format EMBL

 qanxgcgexc Nucleotide OK   OK   OK   GCG format EMBL without prokaryotes

 qanxgcginc Nucleotide OK   OK   OK   GCG format EMBL only prokaryotes

 qasrswww Nucleotide OK   OK   OK   Remote SRS web server

 qawfasta Nucleotide OK   OK   OK   FASTA file wormpep entries

 qawxfasta Nucleotide OK   OK   OK   FASTA file wormpep entries

 qaxembl Nucleotide OK   OK   OK   EMBL flatfiles

 tembl Nucleotide OK   OK   OK   EMBL in native format with EMBL CD-ROM index

 temblall Nucleotide OK   OK   OK   EMBL in native format with EMBL CD-ROM index

 temblrest Nucleotide OK   OK   OK   EMBL in native format with EMBL CD-ROM inde
x

 temblvrt Nucleotide OK   OK   OK   EMBL in native format with EMBL CD-ROM index

 tensembldasgrch37 Nucleotide OK   -    -    Homo_sapiens Reference server based
 on GRCh37 assembly

 testdb Nucleotide OK   OK   OK   test sequence data

 tgb Nucleotide OK   OK   OK   Genbank IDs

 tgenbank Nucleotide OK   OK   OK   GenBank in native format with EMBL CD-ROM in
dex

 tgenedashuman Nucleotide OK   -    -    The Ensembl human Gene_ID reference sou
rce

 tflybase Features OK   -    -

 tgenedb Features OK   -    -

 ttax Taxonomy OK   OK   OK

 taxon Taxonomy OK   OK   OK

 drcat Resource OK   OK   OK

 tedam Obo OK   OK   OK   EDAM using dbxedam test indexes

 tobo Obo OK   OK   OK   EDAM using dbxobo test indexes

 chebi Obo OK   OK   OK

 eco Obo OK   OK   OK

 edam Obo OK   OK   OK

 edam_data Obo OK   OK   OK

 edam_format Obo OK   OK   OK

 edam_identifier Obo OK   OK   OK

 edam_operation Obo OK   OK   OK

 edam_topic Obo OK   OK   OK

 go Obo OK   OK   OK

 go_component Obo OK   OK   OK

 go_function Obo OK   OK   OK

 go_process Obo OK   OK   OK

 pw Obo OK   OK   OK

 ro Obo OK   OK   OK

 so Obo OK   OK   OK

 swo Obo OK   OK   OK




   Example 5

   Display protein databases only:


% showdb -nonucleic
Display information on configured databases

# Name            Type       ID  Qry All Comment
# =============== ========== ==  === === =======
bpsw              Protein    OK  OK  OK
bpworm            Protein    OK  OK  OK
qapblast          Protein    OK  OK  OK  BLAST swissnew
qapblastall       Protein    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, not fi
le 02
qapblastsplitinc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, only f
ile 02
qapfasta          Protein    OK  OK  OK  FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  PIR
qapirall          Protein    OK  OK  OK  PIR
qapirexc          Protein    OK  OK  OK  PIR
qapirinc          Protein    OK  OK  OK  PIR
qapxfasta         Protein    OK  OK  OK  FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  PIR
qaxpirall         Protein    OK  OK  OK  PIR
qaxpirexc         Protein    OK  OK  OK  PIR
qaxpirinc         Protein    OK  OK  OK  PIR
tpir              Protein    OK  OK  OK  PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  Swissprot native format with EMBL CD-RO
M index
tswnew            Protein    OK  OK  OK  SpTrEmbl as 3 files in native format wi
th EMBL CD-ROM index
tflybase          Features   OK  -   -
tgenedb           Features   OK  -   -
ttax              Taxonomy   OK  OK  OK
taxon             Taxonomy   OK  OK  OK
drcat             Resource   OK  OK  OK
tedam             Obo        OK  OK  OK  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  EDAM using dbxobo test indexes
chebi             Obo        OK  OK  OK
eco               Obo        OK  OK  OK
edam              Obo        OK  OK  OK
edam_data         Obo        OK  OK  OK
edam_format       Obo        OK  OK  OK
edam_identifier   Obo        OK  OK  OK
edam_operation    Obo        OK  OK  OK
edam_topic        Obo        OK  OK  OK
go                Obo        OK  OK  OK
go_component      Obo        OK  OK  OK
go_function       Obo        OK  OK  OK
go_process        Obo        OK  OK  OK
pw                Obo        OK  OK  OK
ro                Obo        OK  OK  OK
so                Obo        OK  OK  OK
swo               Obo        OK  OK  OK


   Example 6

   Display the information with no headings:


% showdb -noheading
Display information on configured databases

bpsw              Protein    OK  OK  OK
bpworm            Protein    OK  OK  OK
qapblast          Protein    OK  OK  OK  BLAST swissnew
qapblastall       Protein    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, not fi
le 02
qapblastsplitinc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, only f
ile 02
qapfasta          Protein    OK  OK  OK  FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  PIR
qapirall          Protein    OK  OK  OK  PIR
qapirexc          Protein    OK  OK  OK  PIR
qapirinc          Protein    OK  OK  OK  PIR
qapxfasta         Protein    OK  OK  OK  FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  PIR
qaxpirall         Protein    OK  OK  OK  PIR
qaxpirexc         Protein    OK  OK  OK  PIR
qaxpirinc         Protein    OK  OK  OK  PIR
tpir              Protein    OK  OK  OK  PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  Swissprot native format with EMBL CD-RO
M index
tswnew            Protein    OK  OK  OK  SpTrEmbl as 3 files in native format wi
th EMBL CD-ROM index
bpembl            Nucleotide OK  OK  OK
bpgb              Nucleotide OK  OK  OK
qanfasta          Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall       Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields ind
exed
qanflat           Nucleotide OK  OK  OK  EMBL flatfiles
qanflatall        Nucleotide OK  OK  OK  EMBL flatfiles
qanflatexc        Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc        Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qangcg            Nucleotide OK  OK  OK  GCG format EMBL
qangcgall         Nucleotide OK  OK  OK  GCG format EMBL
qangcgexc         Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc         Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanxfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields ind
exed
qanxflat          Nucleotide OK  OK  OK  EMBL flatfiles
qanxflatall       Nucleotide OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg           Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgall        Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgexc        Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qasrswww          Nucleotide OK  OK  OK  Remote SRS web server
qawfasta          Nucleotide OK  OK  OK  FASTA file wormpep entries
qawxfasta         Nucleotide OK  OK  OK  FASTA file wormpep entries
qaxembl           Nucleotide OK  OK  OK  EMBL flatfiles
tembl             Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblall          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblrest         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblvrt          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
tensembldasgrch37 Nucleotide OK  -   -   Homo_sapiens Reference server based on
GRCh37 assembly
testdb            Nucleotide OK  OK  OK  test sequence data
tgb               Nucleotide OK  OK  OK  Genbank IDs
tgenbank          Nucleotide OK  OK  OK  GenBank in native format with EMBL CD-R
OM index
tgenedashuman     Nucleotide OK  -   -   The Ensembl human Gene_ID reference sou
rce
tflybase          Features   OK  -   -
tgenedb           Features   OK  -   -
ttax              Taxonomy   OK  OK  OK
taxon             Taxonomy   OK  OK  OK
drcat             Resource   OK  OK  OK
tedam             Obo        OK  OK  OK  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  EDAM using dbxobo test indexes
chebi             Obo        OK  OK  OK
eco               Obo        OK  OK  OK
edam              Obo        OK  OK  OK
edam_data         Obo        OK  OK  OK
edam_format       Obo        OK  OK  OK
edam_identifier   Obo        OK  OK  OK
edam_operation    Obo        OK  OK  OK
edam_topic        Obo        OK  OK  OK
go                Obo        OK  OK  OK
go_component      Obo        OK  OK  OK
go_function       Obo        OK  OK  OK
go_process        Obo        OK  OK  OK
pw                Obo        OK  OK  OK
ro                Obo        OK  OK  OK
so                Obo        OK  OK  OK
swo               Obo        OK  OK  OK


   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
qaxpir
qaxpirall
qaxpirexc
qaxpirinc
tpir
tsw
tswnew
bpembl
bpgb
qanfasta
qanfastaall
qanflat
qanflatall
qanflatexc
qanflatinc
qangcg
qangcgall
qangcgexc
qangcginc
qanxfasta
qanxfastaall
qanxflat
qanxflatall
qanxflatexc
qanxflatinc
qanxgcg
qanxgcgall
qanxgcgexc
qanxgcginc
qasrswww
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
bpworm            Protein
qapblast          Protein
qapblastall       Protein
qapblastsplit     Protein
qapblastsplitexc  Protein
qapblastsplitinc  Protein
qapfasta          Protein
qapflat           Protein
qapflatall        Protein
qapir             Protein
qapirall          Protein
qapirexc          Protein
qapirinc          Protein
qapxfasta         Protein
qapxflat          Protein
qaxpir            Protein
qaxpirall         Protein
qaxpirexc         Protein
qaxpirinc         Protein
tpir              Protein
tsw               Protein
tswnew            Protein
bpembl            Nucleotide
bpgb              Nucleotide
qanfasta          Nucleotide
qanfastaall       Nucleotide
qanflat           Nucleotide
qanflatall        Nucleotide
qanflatexc        Nucleotide
qanflatinc        Nucleotide
qangcg            Nucleotide
qangcgall         Nucleotide
qangcgexc         Nucleotide
qangcginc         Nucleotide
qanxfasta         Nucleotide
qanxfastaall      Nucleotide
qanxflat          Nucleotide
qanxflatall       Nucleotide
qanxflatexc       Nucleotide
qanxflatinc       Nucleotide
qanxgcg           Nucleotide
qanxgcgall        Nucleotide
qanxgcgexc        Nucleotide
qanxgcginc        Nucleotide
qasrswww          Nucleotide
qawfasta          Nucleotide
qawxfasta         Nucleotide
qaxembl           Nucleotide
tembl             Nucleotide
temblall          Nucleotide
temblrest         Nucleotide
temblvrt          Nucleotide
tensembldasgrch37 Nucleotide
testdb            Nucleotide
tgb               Nucleotide
tgenbank          Nucleotide
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    Fields
                                                                  Defined  Relea
se Comment
# =============== ========== ==  === === ========= =============================
================================================================= ======== =====
== =======
bpsw              Protein    OK  OK  OK  obda      id,acc
                                                                  special

bpworm            Protein    OK  OK  OK  obda      id
                                                                  special

qapblast          Protein    OK  OK  OK  blast     -
                                                                  special
   BLAST swissnew
qapblastall       Protein    OK  OK  OK  blast     sv,des
                                                                  special
   BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  blast     -
                                                                  special
   BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  blast     -
                                                                  special
   BLAST swissnew split in 5 files, not file 02
qapblastsplitinc  Protein    OK  OK  OK  blast     -
                                                                  special
   BLAST swissnew split in 5 files, only file 02
qapfasta          Protein    OK  OK  OK  emblcd    -
                                                                  special
   FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  emblcd    -
                                                                  special
   SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  emblcd    sv,des,org,key
                                                                  special
   SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  gcg       -
                                                                  special
   PIR
qapirall          Protein    OK  OK  OK  gcg       des,org,key
                                                                  special
   PIR
qapirexc          Protein    OK  OK  OK  gcg       -
                                                                  special
   PIR
qapirinc          Protein    OK  OK  OK  gcg       -
                                                                  special
   PIR
qapxfasta         Protein    OK  OK  OK  emboss    -
                                                                  special
   FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  emboss    -
                                                                  special
   Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  embossgcg -
                                                                  special
   PIR
qaxpirall         Protein    OK  OK  OK  embossgcg des,org,key
                                                                  special
   PIR
qaxpirexc         Protein    OK  OK  OK  embossgcg -
                                                                  special
   PIR
qaxpirinc         Protein    OK  OK  OK  embossgcg -
                                                                  special
   PIR
tpir              Protein    OK  OK  OK  gcg       des,org,key
                                                                  special
   PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  emblcd    id,acc,sv,des,org,key
                                                                  special  36
   Swissprot native format with EMBL CD-ROM index
tswnew            Protein    OK  OK  OK  emblcd    sv,des,org,key
                                                                  special  37
   SpTrEmbl as 3 files in native format with EMBL CD-ROM index
bpembl            Nucleotide OK  OK  OK  obda      id,acc
                                                                  special

bpgb              Nucleotide OK  OK  OK  obda      id,acc
                                                                  special

qanfasta          Nucleotide OK  OK  OK  emblcd    -
                                                                  special
   FASTA file EMBL rodents
qanfastaall       Nucleotide OK  OK  OK  emblcd    sv,des
                                                                  special
   FASTA file EMBL rodents, all fields indexed
qanflat           Nucleotide OK  OK  OK  emblcd    -
                                                                  special
   EMBL flatfiles
qanflatall        Nucleotide OK  OK  OK  emblcd    -
                                                                  special
   EMBL flatfiles
qanflatexc        Nucleotide OK  OK  OK  emblcd    -
                                                                  special
   EMBL flatfiles, no rodent file
qanflatinc        Nucleotide OK  OK  OK  emblcd    -
                                                                  special
   EMBL flatfiles, only rodent file
qangcg            Nucleotide OK  OK  OK  gcg       -
                                                                  special
   GCG format EMBL
qangcgall         Nucleotide OK  OK  OK  gcg       sv,des,org,key
                                                                  special
   GCG format EMBL
qangcgexc         Nucleotide OK  OK  OK  gcg       -
                                                                  special
   GCG format EMBL without prokaryotes
qangcginc         Nucleotide OK  OK  OK  gcg       -
                                                                  special
   GCG format EMBL only prokaryotes
qanxfasta         Nucleotide OK  OK  OK  emboss    -
                                                                  special
   FASTA file EMBL rodents
qanxfastaall      Nucleotide OK  OK  OK  emboss    sv,des
                                                                  special
   FASTA file EMBL rodents, all fields indexed
qanxflat          Nucleotide OK  OK  OK  emboss    id,acc
                                                                  special
   EMBL flatfiles
qanxflatall       Nucleotide OK  OK  OK  emboss    des,org,key,sv
                                                                  special
   EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide OK  OK  OK  emboss    -
                                                                  special
   EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide OK  OK  OK  emboss    -
                                                                  special
   EMBL flatfiles, only rodent file
qanxgcg           Nucleotide OK  OK  OK  embossgcg -
                                                                  special
   GCG format EMBL
qanxgcgall        Nucleotide OK  OK  OK  embossgcg sv,des,org,key
                                                                  special
   GCG format EMBL
qanxgcgexc        Nucleotide OK  OK  OK  embossgcg -
                                                                  special
   GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide OK  OK  OK  embossgcg -
                                                                  special
   GCG format EMBL only prokaryotes
qasrswww          Nucleotide OK  OK  OK  srswww    sv,des,org,key
                                                                  special
   Remote SRS web server
qawfasta          Nucleotide OK  OK  OK  emblcd    -
                                                                  special
   FASTA file wormpep entries
qawxfasta         Nucleotide OK  OK  OK  emboss    -
                                                                  special
   FASTA file wormpep entries
qaxembl           Nucleotide OK  OK  OK  emboss    -
                                                                  special
   EMBL flatfiles
tembl             Nucleotide OK  OK  OK  emblcd    sv,des,org,key
                                                                  special  57
   EMBL in native format with EMBL CD-ROM index
temblall          Nucleotide OK  OK  OK  direct    sv,des,org,key
                                                                  special  57
   EMBL in native format with EMBL CD-ROM index
temblrest         Nucleotide OK  OK  OK  direct    sv,des,org,key
                                                                  special  57
   EMBL in native format with EMBL CD-ROM index
temblvrt          Nucleotide OK  OK  OK  direct    sv,des,org,key
                                                                  special  57
   EMBL in native format with EMBL CD-ROM index
tensembldasgrch37 Nucleotide OK  -   -   das       -
                                                                  special
   Homo_sapiens Reference server based on GRCh37 assembly
testdb            Nucleotide OK  OK  OK  emblcd    des
                                                                  special  01
   test sequence data
tgb               Nucleotide OK  OK  OK  srswww    sv,des,org,key
                                                                  special
   Genbank IDs
tgenbank          Nucleotide OK  OK  OK  emblcd    sv,des,org,key
                                                                  special  01
   GenBank in native format with EMBL CD-ROM index
tgenedashuman     Nucleotide OK  -   -   das       -
                                                                  special
   The Ensembl human Gene_ID reference source
tflybase          Features   OK  -   -   chado(id) uniquename
                                                                  special

tgenedb           Features   OK  -   -   chado(id) uniquename
                                                                  special

ttax              Taxonomy   OK  OK  OK  embosstax id,acc,nam,rnk,up,gc,mgc
                                                                  special

taxon             Taxonomy   OK  OK  OK  embosstax id,acc,tax,rnk,up,gc,mgc
                                                                  standard

drcat             Resource   OK  OK  OK  emboss    id,acc,nam,des,url,cat,edat,e
fmt,eid,etpc,xref,qout,qfmt,qin,qurl,cc,rest,soap,stat,xref,taxid standard

tedam             Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr
,hasin,hasout,isid,isfmt,issrc                                    special  beta1
1  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr
,hasin,hasout,isid,isfmt,issrc                                    special  beta1
1  EDAM using dbxobo test indexes
chebi             Obo        OK  OK  OK  emboss    id,acc,nam,isa,des
                                                                  standard

eco               Obo        OK  OK  OK  emboss    id,acc,nam,isa,des
                                                                  standard

edam              Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr
,hasin,hasout,isid,isfmt,issrc                                    standard

edam_data         Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr
,hasin,hasout,isid,isfmt,issrc                                    standard

edam_format       Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr
,hasin,hasout,isid,isfmt,issrc                                    standard

edam_identifier   Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr
,hasin,hasout,isid,isfmt,issrc                                    standard

edam_operation    Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr
,hasin,hasout,isid,isfmt,issrc                                    standard

edam_topic        Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr
,hasin,hasout,isid,isfmt,issrc                                    standard

go                Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns
                                                                  standard

go_component      Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns
                                                                  standard

go_function       Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns
                                                                  standard

go_process        Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns
                                                                  standard

pw                Obo        OK  OK  OK  emboss    id,acc,nam,isa,des
                                                                  standard

ro                Obo        OK  OK  OK  emboss    id,acc,nam,isa,des
                                                                  standard

so                Obo        OK  OK  OK  emboss    id,acc,nam,isa,des
                                                                  standard

swo               Obo        OK  OK  OK  emboss    id,acc,nam,isa,des
                                                                  standard



Command line arguments

Display information on configured databases
Version: EMBOSS:6.5.6.0

   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
   -full               boolean    [N] Display all columns
   -methods            boolean    [$(full)] This displays the access methods
                                  that can be used on this database, for all,
                                  query or ID access
   -fields             boolean    [$(full)] This displays the search fields
                                  that can be used on this database, other
                                  than the standard 'id' or 'acc' fields.
   -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    [@(!$(only))] Display 'id' column
   -query              boolean    [@(!$(only))] Display 'qry' column
   -all                boolean    [@(!$(only))] Display 'all' column
   -comment            boolean    [@(!$(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


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       ID  Qry All Comment
# =============== ========== ==  === === =======
bpsw              Protein    OK  OK  OK
bpworm            Protein    OK  OK  OK
qapblast          Protein    OK  OK  OK  BLAST swissnew
qapblastall       Protein    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, not fi
le 02
qapblastsplitinc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, only f
ile 02
qapfasta          Protein    OK  OK  OK  FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  PIR
qapirall          Protein    OK  OK  OK  PIR
qapirexc          Protein    OK  OK  OK  PIR
qapirinc          Protein    OK  OK  OK  PIR
qapxfasta         Protein    OK  OK  OK  FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  PIR
qaxpirall         Protein    OK  OK  OK  PIR
qaxpirexc         Protein    OK  OK  OK  PIR
qaxpirinc         Protein    OK  OK  OK  PIR
tpir              Protein    OK  OK  OK  PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  Swissprot native format with EMBL CD-RO
M index
tswnew            Protein    OK  OK  OK  SpTrEmbl as 3 files in native format wi
th EMBL CD-ROM index
bpembl            Nucleotide OK  OK  OK
bpgb              Nucleotide OK  OK  OK
qanfasta          Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall       Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields ind
exed
qanflat           Nucleotide OK  OK  OK  EMBL flatfiles
qanflatall        Nucleotide OK  OK  OK  EMBL flatfiles
qanflatexc        Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc        Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qangcg            Nucleotide OK  OK  OK  GCG format EMBL
qangcgall         Nucleotide OK  OK  OK  GCG format EMBL
qangcgexc         Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc         Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanxfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields ind
exed
qanxflat          Nucleotide OK  OK  OK  EMBL flatfiles
qanxflatall       Nucleotide OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg           Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgall        Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgexc        Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qasrswww          Nucleotide OK  OK  OK  Remote SRS web server
qawfasta          Nucleotide OK  OK  OK  FASTA file wormpep entries
qawxfasta         Nucleotide OK  OK  OK  FASTA file wormpep entries
qaxembl           Nucleotide OK  OK  OK  EMBL flatfiles
tembl             Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblall          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblrest         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
temblvrt          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM
index
tensembldasgrch37 Nucleotide OK  -   -   Homo_sapiens Reference server based on
GRCh37 assembly
testdb            Nucleotide OK  OK  OK  test sequence data
tgb               Nucleotide OK  OK  OK  Genbank IDs
tgenbank          Nucleotide OK  OK  OK  GenBank in native format with EMBL CD-R
OM index
tgenedashuman     Nucleotide OK  -   -   The Ensembl human Gene_ID reference sou
rce
tflybase          Features   OK  -   -
tgenedb           Features   OK  -   -
ttax              Taxonomy   OK  OK  OK
taxon             Taxonomy   OK  OK  OK
drcat             Resource   OK  OK  OK
tedam             Obo        OK  OK  OK  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  EDAM using dbxobo test indexes
chebi             Obo        OK  OK  OK
eco               Obo        OK  OK  OK
edam              Obo        OK  OK  OK
edam_data         Obo        OK  OK  OK
edam_format       Obo        OK  OK  OK
edam_identifier   Obo        OK  OK  OK
edam_operation    Obo        OK  OK  OK
edam_topic        Obo        OK  OK  OK
go                Obo        OK  OK  OK
go_component      Obo        OK  OK  OK
go_function       Obo        OK  OK  OK
go_process        Obo        OK  OK  OK
pw                Obo        OK  OK  OK
ro                Obo        OK  OK  OK
so                Obo        OK  OK  OK
swo               Obo        OK  OK  OK

   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 (c) 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
