EMBOSS: coderet manual

coderet

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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.

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

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

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tembl:x03487

Input files for usage example 2

Database entry: tembl:X03487

Output file format

Output files for usage example

File: x03487.cds

File: x03487.mrna

File: x03487.prot

File: x03487.noncoding

File: x03487.coderet

Output files for usage example 2

File: x03487.coderet

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments