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coderet
Function
Extract CDS, mRNA and translations from feature tables
Description
The feature table of sequence database entries often have sections
like this:
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)
_________________________________________________________________
or:
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)
_________________________________________________________________
or:
This specifies that the translation of the coding region is as
follows.
_________________________________________________________________
FT /translation="MAQDSVDLSCDYQFWMQKLSVWDQASTLETQQDTCLHVAQFQEF
L
FT RKMYEALKEMDSNTVIERFPTIGQLLAKACWNPFILAYDESQKILIWCLCCLINKEPQ
N
FT SGQSKLNSWIQGVLSHILSALRFDKEVALFTQGLGYAPIDYYPGLLKNMVLSLASELR
E
FT NHLNGFNTQRRMAPERVASLSRVCVPLITLTDVDPLVEALLICHGREPQEILQPEFFE
A
FT VNEAILLKKISLPMSAVVCLWLRHLPSLEKAMLHLFEKLISSERNCLRRIECFIKDSS
L
FT PQAACHPAIFRVDEMFRCALLETDGALEIIATIQVFTQCFVEALEKASKQLRFALKTY
F
FT PYTSPSLAMVLLQDPQDIPRGHWLQTLKHISELLREAVEDQTHGSCGGPFESWFLFIH
F
FT GGWAEMVAEQLLMSAAEPPTALLWLLAFYYGPRDGRQQRAQTMVQVKAVLGHLLAMSR
S
FT SSLSAQDLQTVAGQGTDTDLRAPAQQLIRHLLLNFLLWAPGGHTIAWDVITLMAHTAE
I
FT THEIIGFLDQTLYRWNRLGIESPRSEKLARELLKELRTQV"
_________________________________________________________________
It is often a tedious and error-prone job to extract the several
sections of these sequences from the database entries and to join them
together to construct the indicated finished sequence.
coderet does this job for you.
You specify the sequence containing the feature table and it extracts
the required CDS, mRNA and/or protein sequences specified by this
feature table. If any sequences are in other entries of that database,
they are automatically fetched and incorporated correctly into the
final sequence.
The translations are not made from the coding sequence, they are
extracted directly from the translation sequence held in the feature
table.
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
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
-sformat1 string Input sequence format
-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 standard output
-filter boolean Read standard input, write 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. 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
Input file format
coderet reads one or more nucleic sequence USAs having CDS, mRNA or
translation headings in their feature tables.
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 EPD; EP11112; HS_FTH1.
DR RFAM; RF00037.
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="PDB:1FHA"
FT /db_xref="PDB:2FHA"
FT /db_xref="UniProtKB/Swiss-Prot:P02794"
FT /protein_id="CAA27205.1"
FT /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDR
D
FT DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMEC
A
FT LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAP
E
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 6
0
gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt 12
0
ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca 18
0
gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg 24
0
gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg 30
0
caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc 36
0
gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga 42
0
actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct 48
0
cctacgttta cctgtccatg gtgagcgcgg gc 51
2
//
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 EPD; EP11112; HS_FTH1.
DR RFAM; RF00037.
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="PDB:1FHA"
FT /db_xref="PDB:2FHA"
FT /db_xref="UniProtKB/Swiss-Prot:P02794"
FT /protein_id="CAA27205.1"
FT /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDR
D
FT DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMEC
A
FT LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAP
E
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 6
0
gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt 12
0
ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca 18
0
gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg 24
0
gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg 30
0
caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc 36
0
gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga 42
0
actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct 48
0
cctacgttta cctgtccatg gtgagcgcgg gc 51
2
//
Output file format
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
'HSXYZ' would be named 'HSXYZ_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 2 1 5 X03487
Output files for usage example 2
File: x03487.coderet
mRNA Total Sequence
===== ===== ========
1 1 X03487
Data files
None.
Notes
The translations are not made from the coding sequence, they are
extracted directly from the translation sequence held in the feature
table.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
backtranambig Back translate a protein sequence to ambiguous codons
backtranseq Back translate a protein sequence
extractfeat Extract features from a sequence
maskfeat Mask off features of a sequence
plotorf Plot potential open reading frames
prettyseq Output sequence with translated ranges
remap Display sequence with restriction sites, translation etc
showfeat Show features of a sequence
showorf Pretty output of DNA translations
showseq Display a sequence with features, translation etc
sixpack Display a DNA sequence with 6-frame translation and ORFs
transeq Translate nucleic acid sequences
twofeat Finds neighbouring pairs of features in sequences
Author(s)
Alan Bleasby (ajb ebi.ac.uk)
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
|
