| coderet

## Wiki

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Please help by correcting and extending the Wiki pages.

## Function

Extract CDS, mRNA and translations from feature tables

## Description

coderet extracts the coding nucleotide sequence (CDS), messenger RNA nucleotide sequence (mRNA) and translations specified by the feature tables of the input sequence(s). If the sequences to be extracted are in other entries of that database, they are automatically fetched and incorporated correctly into the output.

For each input sequence, an output sequence file is written containing any CDS, mRNA and protein translation sequences from the input feature table. Optionally, the CDS, mRNA, translated protein sequence and non-coding nucleotide sequence regions may be written to separate files.

## Usage

Here is a sample session with coderet

To extract all of the CDS, mRNA, non-coding and the protein translations:

    % coderet
    Extract CDS, mRNA and translations from feature tables
    Input nucleotide sequence(s): tembl:x03487
    Output file [x03487.coderet]:
    Coding nucleotide output sequence(s) (optional) [x03487.cds]:
    Messenger RNA nucleotide output sequence(s) (optional) [x03487.mrna]:
    Translated coding protein output sequence(s) (optional) [x03487.prot]:
    Non-coding nucleotide output sequence(s) (optional) [x03487.noncoding]:

Go to the input files for this example
Go to the output files for this example

Example 2

To only extract the mRNA sequence:

    % coderet -nocds -notranslation -norest
    Extract CDS, mRNA and translations from feature tables
    Input nucleotide sequence(s): tembl:X03487
    Output file [x03487.coderet]:
    Messenger RNA nucleotide output sequence(s) (optional) [x03487.mrna]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Extract CDS, mRNA and translations from feature tables
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-seqall]            seqall     Nucleotide sequence(s) filename and optional
                                      format, or reference (input USA)
      [-outfile]           outfile    [*.coderet] Output file name
      [-cdsoutseq]         seqoutall  [.] Coding nucleotide
                                      output sequence(s) (optional)
      [-mrnaoutseq]        seqoutall  [.] Messenger RNA
                                      nucleotide output sequence(s) (optional)
      [-translationoutseq] seqoutall  [.] Translated coding
                                      protein output sequence(s) (optional)
      [-restoutseq]        seqoutall  [.] Non-coding nucleotide
                                      output sequence(s) (optional)

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-seqall" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -scircular1         boolean    Sequence is circular
       -squick1            boolean    Read id and sequence only
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outfile" associated qualifiers
       -odirectory2        string     Output directory

       "-cdsoutseq" associated qualifiers
       -osformat3          string     Output seq format
       -osextension3       string     File name extension
       -osname3            string     Base file name
       -osdirectory3       string     Output directory
       -osdbname3          string     Database name to add
       -ossingle3          boolean    Separate file for each entry
       -oufo3              string     UFO features
       -offormat3          string     Features format
       -ofname3            string     Features file name
       -ofdirectory3       string     Output directory

       "-mrnaoutseq" associated qualifiers
       -osformat4          string     Output seq format
       -osextension4       string     File name extension
       -osname4            string     Base file name
       -osdirectory4       string     Output directory
       -osdbname4          string     Database name to add
       -ossingle4          boolean    Separate file for each entry
       -oufo4              string     UFO features
       -offormat4          string     Features format
       -ofname4            string     Features file name
       -ofdirectory4       string     Output directory

       "-translationoutseq" associated qualifiers
       -osformat5          string     Output seq format
       -osextension5       string     File name extension
       -osname5            string     Base file name
       -osdirectory5       string     Output directory
       -osdbname5          string     Database name to add
       -ossingle5          boolean    Separate file for each entry
       -oufo5              string     UFO features
       -offormat5          string     Features format
       -ofname5            string     Features file name
       -ofdirectory5       string     Output directory

       "-restoutseq" associated qualifiers
       -osformat6          string     Output seq format
       -osextension6       string     File name extension
       -osname6            string     Base file name
       -osdirectory6       string     Output directory
       -osdbname6          string     Database name to add
       -ossingle6          boolean    Separate file for each entry
       -oufo6              string     UFO features
       -offormat6          string     Features format
       -ofname6            string     Features file name
       -ofdirectory6       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
[-seqall] (Parameter 1) | seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-outfile] (Parameter 2) | outfile | Output file name | Output file | <*>.coderet
[-cdsoutseq] (Parameter 3) | seqoutall | Coding nucleotide output sequence(s) (optional) | Writeable sequence(s) | <*>.format
[-mrnaoutseq] (Parameter 4) | seqoutall | Messenger RNA nucleotide output sequence(s) (optional) | Writeable sequence(s) | <*>.format
[-translationoutseq] (Parameter 5) | seqoutall | Translated coding protein output sequence(s) (optional) | Writeable sequence(s) | <*>.format
[-restoutseq] (Parameter 6) | seqoutall | Non-coding nucleotide output sequence(s) (optional) | Writeable sequence(s) | <*>.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-seqall" associated seqall qualifiers
-sbegin1 -sbegin_seqall | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_seqall | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_seqall | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_seqall | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_seqall | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_seqall | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_seqall | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_seqall | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_seqall | boolean | Sequence is circular | Boolean value Yes/No | N
-squick1 -squick_seqall | boolean | Read id and sequence only | Boolean value Yes/No | N
-sformat1 -sformat_seqall | string | Input sequence format | Any string |
-iquery1 -iquery_seqall | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_seqall | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_seqall | string | Database name | Any string |
-sid1 -sid_seqall | string | Entryname | Any string |
-ufo1 -ufo_seqall | string | UFO features | Any string |
-fformat1 -fformat_seqall | string | Features format | Any string |
-fopenfile1 -fopenfile_seqall | string | Features file name | Any string |
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile | string | Output directory | Any string |
"-cdsoutseq" associated seqoutall qualifiers
-osformat3 -osformat_cdsoutseq | string | Output seq format | Any string |
-osextension3 -osextension_cdsoutseq | string | File name extension | Any string | cds
-osname3 -osname_cdsoutseq | string | Base file name | Any string |
-osdirectory3 -osdirectory_cdsoutseq | string | Output directory | Any string |
-osdbname3 -osdbname_cdsoutseq | string | Database name to add | Any string |
-ossingle3 -ossingle_cdsoutseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo3 -oufo_cdsoutseq | string | UFO features | Any string |
-offormat3 -offormat_cdsoutseq | string | Features format | Any string |
-ofname3 -ofname_cdsoutseq | string | Features file name | Any string |
-ofdirectory3 -ofdirectory_cdsoutseq | string | Output directory | Any string |
"-mrnaoutseq" associated seqoutall qualifiers
-osformat4 -osformat_mrnaoutseq | string | Output seq format | Any string |
-osextension4 -osextension_mrnaoutseq | string | File name extension | Any string | mrna
-osname4 -osname_mrnaoutseq | string | Base file name | Any string |
-osdirectory4 -osdirectory_mrnaoutseq | string | Output directory | Any string |
-osdbname4 -osdbname_mrnaoutseq | string | Database name to add | Any string |
-ossingle4 -ossingle_mrnaoutseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo4 -oufo_mrnaoutseq | string | UFO features | Any string |
-offormat4 -offormat_mrnaoutseq | string | Features format | Any string |
-ofname4 -ofname_mrnaoutseq | string | Features file name | Any string |
-ofdirectory4 -ofdirectory_mrnaoutseq | string | Output directory | Any string |
"-translationoutseq" associated seqoutall qualifiers
-osformat5 -osformat_translationoutseq | string | Output seq format | Any string |
-osextension5 -osextension_translationoutseq | string | File name extension | Any string | prot
-osname5 -osname_translationoutseq | string | Base file name | Any string |
-osdirectory5 -osdirectory_translationoutseq | string | Output directory | Any string |
-osdbname5 -osdbname_translationoutseq | string | Database name to add | Any string |
-ossingle5 -ossingle_translationoutseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo5 -oufo_translationoutseq | string | UFO features | Any string |
-offormat5 -offormat_translationoutseq | string | Features format | Any string |
-ofname5 -ofname_translationoutseq | string | Features file name | Any string |
-ofdirectory5 -ofdirectory_translationoutseq | string | Output directory | Any string |
"-restoutseq" associated seqoutall qualifiers
-osformat6 -osformat_restoutseq | string | Output seq format | Any string |
-osextension6 -osextension_restoutseq | string | File name extension | Any string | noncoding
-osname6 -osname_restoutseq | string | Base file name | Any string |
-osdirectory6 -osdirectory_restoutseq | string | Output directory | Any string |
-osdbname6 -osdbname_restoutseq | string | Database name to add | Any string |
-ossingle6 -ossingle_restoutseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo6 -oufo_restoutseq | string | UFO features | Any string |
-offormat6 -offormat_restoutseq | string | Features format | Any string |
-ofname6 -ofname_restoutseq | string | Features file name | Any string |
-ofdirectory6 -ofdirectory_restoutseq | 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

coderet reads one or more nucleic sequences having CDS, mRNA or translation headings in their feature tables.

The input is a standard EMBOSS sequence query (also known as a 'USA') with associated feature information.

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: text, html, xml (uniprotxml), obo, embl (swissprot)

Where the sequence format has no feature information, a second file can be read to load the feature data. The file is specified with the qualifier `-ufo xxx` and the feature format is specified with the qualifier `-fformat xxx`

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

See: http://emboss.sf.net/docs/themes/FeatureFormats.html for further information on feature formats.

### Input files for usage example

'tembl:x03487' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:x03487

    ID   X03487; SV 1; linear; genomic DNA; STD; HUM; 512 BP.
    XX
    AC   X03487;
    XX
    DT   02-JUL-1986 (Rel. 09, Created)
    DT   24-AUG-2005 (Rel. 84, Last updated, Version 3)
    XX
    DE   Human apoferritin H gene exon 1
    XX
    KW   ferritin.
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
    OC   Homo.
    XX
    RN   [1]
    RP   1-512
    RX   DOI; 10.1093/nar/14.2.721.
    RX   PUBMED; 3003694.
    RA   Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R.,
    RA   Delius H., Cortese R.;
    RT   "Structure of gene and pseudogenes of human apoferritin H";
    RL   Nucleic Acids Res. 14(2):721-736(1986).
    XX
    DR   Ensembl-Gn; ENSG00000167996; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000273550; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000406545; Homo_sapiens.
    DR   RFAM; RF00037; IRE.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..512
    FT                   /organism="Homo sapiens"
    FT                   /mol_type="genomic DNA"
    FT                   /db_xref="taxon:9606"
    FT   misc_feature    65..70
    FT                   /note="GGGCGG box"
    FT   misc_feature    103..108
    FT                   /note="GGGCGG box"
    FT   misc_feature    126..131
    FT                   /note="GGGCGG box"
    FT   promoter        150..154
    FT                   /note="put. TATA box"
    FT   mRNA            179..500
    FT                   /note="exon 1"
    FT   CDS             join(387..500,X03488.1:50..196,X03488.1:453..578,
    FT                   X03488.1:674..838)
    FT                   /product="apoferritin H subunit"
    FT                   /db_xref="GDB:120617"
    FT                   /db_xref="GOA:P02794"
    FT                   /db_xref="HGNC:3976"
    FT                   /db_xref="InterPro:IPR001519"
    FT                   /db_xref="InterPro:IPR008331"
    FT                   /db_xref="InterPro:IPR009040"
    FT                   /db_xref="InterPro:IPR009078"
    FT                   /db_xref="InterPro:IPR012347"
    FT                   /db_xref="InterPro:IPR014034"
    FT                   /db_xref="PDB:1FHA"
    FT                   /db_xref="PDB:2CEI"
    FT                   /db_xref="PDB:2CHI"
    FT                   /db_xref="PDB:2CIH"
    FT                   /db_xref="PDB:2CLU"
    FT                   /db_xref="PDB:2CN6"
    FT                   /db_xref="PDB:2CN7"
    FT                   /db_xref="PDB:2FHA"
    FT                   /db_xref="PDB:2IU2"
    FT                   /db_xref="PDB:2Z6M"
    FT                   /db_xref="PDB:3AJO"
    FT                   /db_xref="PDB:3AJP"
    FT                   /db_xref="PDB:3AJQ"
    FT                   /db_xref="PDB:3ERZ"
    FT                   /db_xref="PDB:3ES3"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P02794"
    FT                   /protein_id="CAA27205.1"
    FT                   /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD
    FT                   DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA
    FT                   LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE
    FT                   SGLAEYLFDKHTLGDSDNES"
    FT   intron          501..>512
    FT                   /note="intron I"
    XX
    SQ   Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
         agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca        60
         gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt       120
         ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca       180
         gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg       240
         gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg       300
         caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc       360
         gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga       420
         actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct       480
         cctacgttta cctgtccatg gtgagcgcgg gc                                     512
    //

### Input files for usage example 2

### Database entry: tembl:X03487

    ID   X03487; SV 1; linear; genomic DNA; STD; HUM; 512 BP.
    XX
    AC   X03487;
    XX
    DT   02-JUL-1986 (Rel. 09, Created)
    DT   24-AUG-2005 (Rel. 84, Last updated, Version 3)
    XX
    DE   Human apoferritin H gene exon 1
    XX
    KW   ferritin.
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
    OC   Homo.
    XX
    RN   [1]
    RP   1-512
    RX   DOI; 10.1093/nar/14.2.721.
    RX   PUBMED; 3003694.
    RA   Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R.,
    RA   Delius H., Cortese R.;
    RT   "Structure of gene and pseudogenes of human apoferritin H";
    RL   Nucleic Acids Res. 14(2):721-736(1986).
    XX
    DR   Ensembl-Gn; ENSG00000167996; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000273550; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000406545; Homo_sapiens.
    DR   RFAM; RF00037; IRE.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..512
    FT                   /organism="Homo sapiens"
    FT                   /mol_type="genomic DNA"
    FT                   /db_xref="taxon:9606"
    FT   misc_feature    65..70
    FT                   /note="GGGCGG box"
    FT   misc_feature    103..108
    FT                   /note="GGGCGG box"
    FT   misc_feature    126..131
    FT                   /note="GGGCGG box"
    FT   promoter        150..154
    FT                   /note="put. TATA box"
    FT   mRNA            179..500
    FT                   /note="exon 1"
    FT   CDS             join(387..500,X03488.1:50..196,X03488.1:453..578,
    FT                   X03488.1:674..838)
    FT                   /product="apoferritin H subunit"
    FT                   /db_xref="GDB:120617"
    FT                   /db_xref="GOA:P02794"
    FT                   /db_xref="HGNC:3976"
    FT                   /db_xref="InterPro:IPR001519"
    FT                   /db_xref="InterPro:IPR008331"
    FT                   /db_xref="InterPro:IPR009040"
    FT                   /db_xref="InterPro:IPR009078"
    FT                   /db_xref="InterPro:IPR012347"
    FT                   /db_xref="InterPro:IPR014034"
    FT                   /db_xref="PDB:1FHA"
    FT                   /db_xref="PDB:2CEI"
    FT                   /db_xref="PDB:2CHI"
    FT                   /db_xref="PDB:2CIH"
    FT                   /db_xref="PDB:2CLU"
    FT                   /db_xref="PDB:2CN6"
    FT                   /db_xref="PDB:2CN7"
    FT                   /db_xref="PDB:2FHA"
    FT                   /db_xref="PDB:2IU2"
    FT                   /db_xref="PDB:2Z6M"
    FT                   /db_xref="PDB:3AJO"
    FT                   /db_xref="PDB:3AJP"
    FT                   /db_xref="PDB:3AJQ"
    FT                   /db_xref="PDB:3ERZ"
    FT                   /db_xref="PDB:3ES3"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P02794"
    FT                   /protein_id="CAA27205.1"
    FT                   /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD
    FT                   DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA
    FT                   LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE
    FT                   SGLAEYLFDKHTLGDSDNES"
    FT   intron          501..>512
    FT                   /note="intron I"
    XX
    SQ   Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
         agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca        60
         gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt       120
         ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca       180
         gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg       240
         gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg       300
         caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc       360
         gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga       420
         actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct       480
         cctacgttta cctgtccatg gtgagcgcgg gc                                     512
    //

## Output file format

The output is a standard EMBOSS sequence file.

The results can be output in one of several styles by using the command-line qualifier `-osformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

The output is a sequence file containing any CDS, mRNA and protein translation sequences as specified by the feature table of the sequence(s).

One or more of CDS, mRNA, translation can be excluded from the output by using the appropriate qualifiers to the program (i.e. `-nocds`, etc.)

The ID names of the output sequences are constructed from the name of the input sequence, the type of feature being output (i.e. cds, mrna, pro) and a unique ordinal number for this type to distinguish it from others in this sequence. The name, type and number of separated by underscore characters. Thus the second CDS feature in the sequence 'A12345' would be named 'A12345_cds_2'.

The translations are not made from the coding sequence, they are extracted directly from the translation sequence held in the feature table.

### Output files for usage example

### File: x03487.cds

    >x03487_cds_1
    atgacgaccgcgtccacctcgcaggtgcgccagaactaccaccaggactcagaggccgcc
    atcaaccgccagatcaacctggagctctacgcctcctacgtttacctgtccatgtcttac
    tactttgaccgcgatgatgtggctttgaagaactttgccaaatactttcttcaccaatct
    catgaggagagggaacatgctgagaaactgatgaagctgcagaaccaacgaggtggccga
    atcttccttcaggatatcaagaaaccagactgtgatgactgggagagcgggctgaatgca
    atggagtgtgcattacatttggaaaaaaatgtgaatcagtcactactggaactgcacaaa
    ctggccactgacaaaaatgacccccatttgtgtgacttcattgagacacattacctgaat
    gagcaggtgaaagccatcaaagaattgggtgaccacgtgaccaacttgcgcaagatggga
    gcgcccgaatctggcttggcggaatatctctttgacaagcacaccctgggagacagtgat
    aatgaaagctaa

### File: x03487.mrna

    >x03487_mrna_1
    cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc
    cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac
    cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg
    ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca
    gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc
    ctcctacgtttacctgtccatg

### File: x03487.prot

    >x03487_pro_1
    MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
    HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHK
    LATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSD
    NES

### File: x03487.noncoding

    >x03487_noncoding_1
    agnncaaacctnagctccgccagagcgcgcgaggcctccagcggccgcccctcccccaca
    gcaggggcggggntcccgcgcccaccggaaggagcgggctcggggcgggcggcgctgatt
    ggccggggcgggcctgacgccgacgcggctataagagaccacaagcgacccgcagggc
    >x03487_noncoding_501
    gtgagcgcgggc

### File: x03487.coderet

       CDS  mRNA non-c Trans Total Sequence
     ===== ===== ===== ===== ===== ========
         1     1     6     1     8 X03487

### Output files for usage example 2

### File: x03487.coderet

      mRNA Total Sequence
     ===== ===== ========
         1     1 X03487

## Data files

None.

## Notes

One or more of CDS, mRNA, translation or non-coding regions can be excluded from output with the appropriate qualifiers; "no" is prepended to the qualifier name, for example `-nocds` would exclude the coding sequence.

The translations are not made from the coding sequence, they are extracted directly from the translation sequence held in the feature table.

The regions of the feature table that concern us are shown below.

This specifies that the coding sequence for the gene is constructed by joining several sections of code, many of which are in other entries in this database:

    FT   CDS             join(U21925.1:818..987,U21926.1:258..420,
    FT                   U21927.1:428..520,U21928.1:196..336,U21929.1:279..415,
    FT                   U21930.1:895..1014,516..708)

This specifies that the messenger RNA sequence for the gene is constructed by joining several sections of code, many of which are in other entries in this database.

    FT   mRNA            join(M88628.1:1006..1318,M88629.1:221..342,
    FT                   M88630.1:101..223,M88631.1:46..258,M88632.1:104..172,
    FT                   M88633.1:387..503,M88634.1:51..272,M88635.1:303..564,
    FT                   M88635.1:849..1020,M88636.1:282..375,M88637.1:39..253,
    FT                   M88638.1:91..241,M88639.1:168..377,M88640.1:627..3732,
    FT                   M88641.1:158..311,M88642.1:1051..1263,M88642.1:1550..1778,
    FT                   M88642.1:1986..2168,M88642.1:3904..4020,
    FT                   M88642.1:4627..4698,M88643.1:39..124,M88644.1:42..197,
    FT                   M88645.1:542..686,M88646.1:75..223,M88647.1:109..285,
    FT                   253..2211)

This specifies that the translation of the coding region is as follows:

    FT                   /translation="MAQDSVDLSCDYQFWMQKLSVWDQASTLETQQDTCLHVAQFQEFL
    FT                   RKMYEALKEMDSNTVIERFPTIGQLLAKACWNPFILAYDESQKILIWCLCCLINKEPQN
    FT                   SGQSKLNSWIQGVLSHILSALRFDKEVALFTQGLGYAPIDYYPGLLKNMVLSLASELRE
    FT                   NHLNGFNTQRRMAPERVASLSRVCVPLITLTDVDPLVEALLICHGREPQEILQPEFFEA
    FT                   VNEAILLKKISLPMSAVVCLWLRHLPSLEKAMLHLFEKLISSERNCLRRIECFIKDSSL
    FT                   PQAACHPAIFRVDEMFRCALLETDGALEIIATIQVFTQCFVEALEKASKQLRFALKTYF
    FT                   PYTSPSLAMVLLQDPQDIPRGHWLQTLKHISELLREAVEDQTHGSCGGPFESWFLFIHF
    FT                   GGWAEMVAEQLLMSAAEPPTALLWLLAFYYGPRDGRQQRAQTMVQVKAVLGHLLAMSRS
    FT                   SSLSAQDLQTVAGQGTDTDLRAPAQQLIRHLLLNFLLWAPGGHTIAWDVITLMAHTAEI
    FT                   THEIIGFLDQTLYRWNRLGIESPRSEKLARELLKELRTQV"

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
abiview | Display the trace in an ABI sequencer file
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
checktrans | Report STOP codons and ORF statistics of a protein
entret | Retrieve sequence entries from flatfile databases and files
extractalign | Extract regions from a sequence alignment
infoalign | Display basic information about a multiple sequence alignment
infoseq | Display basic information about sequences
plotorf | Plot potential open reading frames in a nucleotide sequence
prettyseq | Write a nucleotide sequence and its translation to file
refseqget | Get reference sequence
remap | Display restriction enzyme binding sites in a nucleotide sequence
seqxref | Retrieve all database cross-references for a sequence entry
seqxrefget | Retrieve all cross-referenced data for a sequence entry
showalign | Display a multiple sequence alignment in pretty format
showorf | Display a nucleotide sequence and translation in pretty format
showseq | Display sequences with features in pretty format
sixpack | Display a DNA sequence with 6-frame translation and ORFs
transeq | Translate nucleic acid sequences
variationget | Get sequence variations
whichdb | Search all sequence databases for an entry and retrieve it

## Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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

## History

Written (Nov 2000) - Alan Bleasby.

## Target users

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

## Comments

None