ONIP(1)                     OGMP SEQUENCE UTILITIES                  ONIP(1)

NAME
   onip - ogmp interface to nip, permitting batch-wise codon usage analysis 

SYNOPSIS
   onip [-g gcode] [-o outfile] [pepper switches] mf
 
DESCRIPTION
   Onip is the ogmp interface to nip. Its purpose is to permit batch 
   translation of an input file that contains nucleotide sequences and 
   obtain the resulting codon tables (see nip(1)). The input file can be 
   in masterfile or fasta format, i.e., a header line is required. 

   The basic mitochondrial genetic code is assumed by nip for the translation
   (code #20), but it can be changed to any other code (see 
   /share/supported/apps/ncbi/data/gc.prt or run gcshow). Furthermore,
   deviations can be imposed on the chosen genetic code with the "-d"
   option (see OPTIONS).

   Onip uses pepper(1) to extract the regions it should consider for codon 
   usage. It is possible to pass to onip most of the switches recognized by
   pepper (e.g. -X, -p, -n, -a, -i, etc...). Consult pepper's manpage for a 
   complete description of these switches.

   By default onip writes its output in a file called onip.out, but -o (see
   OPTIONS) can be used to specify another file name.


OPTIONS
   -g code
     Use the genetic code "code" to perform translation. "code" can be any 
     valid NCBI genetic code number (e.g. 1, 19). Refer to 
     /share/supported/apps/ogmp/lib/NCBI/data/gc.prt (3) to see the valid
     identifiers. If -g is not supplied, onip will consult
     /share/supported/apps/ogmp/lib/genome_name.lst (see FILES) in order to
     find the genetic code associated to the masterfile's base name. If there
     is no genetic code supplied either on the command line (with -g) or in
     the file /share/supported/apps/ogmp/lib/genome_name.lst, onip will use the
     basic mitochondrial code (number 20 in
     /share/supported/apps/ncbi/data/gc.prt). 

   -d deviation
       Apply deviation to the genetic code. Deviation must have the form
       "Tga=w,ttt=l,AAA=a" (ie no spaces, comma-separated list of codon 
       reassignments). All codons must contain only the letters A,C,G,T and the
       valid amino acids are: F,L,I,M,V,S,P,T,A,Y,*,H,Q,N,K,D,E,C,W,R,S,G. Onip
       always ignores the casing of these informations.

   -o outfile
      Write the codon usage tables in file outfile, instead of the default
      onip.out.


FILES
   /share/supported/apps/staden_1999.0/bin/nip
       The program for which onip is an interface
   /share/supported/apps/ogmp/lib/genome_name.lst
       All the masterfiles, with their properties
   /share/supported/apps/ogmp/bin/pepper
       Used to extract the regions to consider for codon usage

SEE ALSO
   nip(1), pepper(1)
 
AUTHOR
   Gertraud Burger (initial idea and specs)
   Nicolas Brossard (program design and coding)

Organelle Genome Megasequencing Project 1999