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gp_seq2prot
Langue: en
Version: 111690 (mandriva - 01/05/08)
Section: 1 (Commandes utilisateur)
NAME
gp_seq2prot - translate DNA/RNA to protein sequenceSYNOPSIS
gp_seq2prot [-p] [-c code_file ] [-q] [-v] [-d] [-h] [inputfile] [outputfile]OPTIONS
- -p
- print the codon table and exit
- -c code_file
- load codon table modifications from file code_file
- -v
- Prints the version information.
- -d
- Prints lots of debugging information.
- -h
- Shows usage information.
- inputfile
- file to proces; if not given, will use standard input
- outputfile
- file to write the data to; if not given, will use standard output
DESCRIPTION
gp_seq2prot tries to translate a DNA / RNA sequence into protein sequence. As a default, it uses the standard translation table common for most organisms, but you can load your own defaults from a file using option -c. The format of this file is quite simple: all empty lines or lines starting with a "#" are ignored; all other lines are supposed to contain a three letter codon, space, and one letter amino acid code or '0' for a STOP codon. You can see the full codon table with the option -p.
The sequences are supposed to begin with a start codon, but their ends may vary: if no stop codon is found before the sequence ends, a warning message is generated, but the output will not be aborted.
EXAMPLES
- o
- Translate sequences from file all.orfs.fasta into protein using the mycoplasma translation table modification stored in file myco.cdn:
- gp_seq2prot -c myco.cdn all.orfs.fasta
- o
- Sample file containing modifications of the translation table:
-
# This is the codon table for Mycoplasma pneumoniae # As you see, you have only to put down the codons which differ from the # standard code. Blank lines, tabs, and lines starting with a '#' are # always skipped. UGA W
SEE ALSO
Genpak(1) gp_acc(1) gp_adjust(1) gp_cdndev(1) gp_cusage(1) gp_digest(1) gp_dimer(1) gp_findorf(1) gp_gc(1) gp_getseq(1) gp_map(1) gp_matrix(1) gp_mkmtx(1) gp_pattern(1) gp_primer(1) gp_qs(1) gp_randseq(1) gp_slen(1) gp_tm(1) gp_trimer(1)DIAGNOSTICS
All Genpak programs complain in situations you would also complain, like when they cannot find a sequence you gave them or the sequence is not valid.
The Genpak programs do not write over existing files. I have found this feature very useful :-)
BUGS
I'm sure there are plenty left, so please mail me if you find them. I tried to clean up every bug I could find.
AUTHOR
January Weiner III <january@bioinformatics.org>
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre