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coderet
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
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
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 (c) 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
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