Appdoc:Coderet

From EMBOSS

Contents 1 Function 2 Description 3 Usage 4 Command line arguments 5 Input file format 5.1 Input example 5.1.1 Database entry: tembl:x03487 5.2 Input example 2 5.2.1 Database entry: tembl:X03487 6 Output file format 6.1 Output example 6.1.1 File: x03487.cds 6.1.2 File: x03487.mrna 6.1.3 File: x03487.prot 6.1.4 File: x03487.noncoding 6.1.5 File: x03487.coderet 6.2 Output example 2 6.2.1 File: x03487.coderet 7 Data files 8 Notes 9 References 10 Warnings 11 Diagnostic Error Messages 12 Exit status 13 Known bugs 14 See also 15 Author(s) 16 History 17 Target users 18 Comments

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

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
-sformat1 -sformat_seqall	string	Input sequence format	Any string
-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. 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

Input file format

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

Input 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; 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:IPR014034"
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 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; 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:IPR014034"
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 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 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 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

backtranambig	Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq	Back-translate a protein sequence to a nucleotide sequence
extractfeat	Extract features from sequence(s)
maskfeat	Write a sequence with masked features
plotorf	Plot potential open reading frames in a nucleotide sequence
prettyseq	Write a nucleotide sequence and its translation to file
remap	Display restriction enzyme binding sites in a nucleotide sequence
showfeat	Display features of a sequence in pretty format
showorf	Display a nucleotide sequence and translation in pretty format
showseq	Displays sequences with features in pretty format
sixpack	Display a DNA sequence with 6-frame translation and ORFs
transeq	Translate nucleic acid sequences
twofeat	Finds neighbouring pairs of features in sequence(s)

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