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gp_cusage

Langue: en

Version: 111678 (mandriva - 01/05/08)

Section: 1 (Commandes utilisateur)

NAME

gp_cusage - print codon usage of sequence(s)

SYNOPSIS

gp_cusage [-c table_file ] [-p] [-q] [-v] [-d] [-h] [-?] [inputfile] [outputfile]

OPTIONS

-c table_file
Uses alternate codon table.
-p
Nicely prints the codon table & exits gracefully.
-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_cusage sources one or more DNA or RNA sequence files and prints the total percentual frequencies of all codons. The sequences have to begin with a start codon, but if they are incomplete (i.e. end before the stop codon is read) only a warning is issued.

EXAMPLES

o
to print the codon usage of the fasta sequences contained in the file orfs.fasta, type
gp_cusage orfs.fasta
o
to print the codon usage of a protein sequence located at genome positions 15843 14602 in the sequence Mpneu.fasta, type
getseq 15843 14602 Mpneu.fasta | gp_cusage

SEE ALSO

Genpak(1) gp_acc(1) gp_adjust(1) gp_cdndev(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_seq2prot(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>

UN,

Soit Un virgule ou point six cent dix-huit ; ainsi
Indique-t-on volontiers, en l'arrondissant,
X tel qu'égal à son inverse plus un, si !

Ce rapport supposé divin, éblouissant,
Est aussi naturel chez les Fibonensi*,
Nombre dit d'or depuis Léonard de Vinci,
Tau ou Phi pour certains érudits plus récents.

Du nombre jaune, ambré comme un maravédis,
Il en rêva, René, l'an mil six cent dix-huit,
Xanthoptique** somme où "ergo sum" fut prédit.

Harmonieusement ce poème est construit
Uniquement sur des nombres m de mots dits.
Il y a t total du sonnet, soit cent dix,
Tandis que k au ratio est soixante-huit.

-- Schulz, Rémi