no_fasta(1)                   OGMP SEQUENCE UTILITIES                no_fasta(1)

NAME
  no_fasta - run fasta on selected orfs in a masterfile

SYNOPSIS
  no_fasta [-g gcode] [-l length] [-F num] [-o ocode] [-O outfile]
          [-a nb_align] [-s nb_scores]  masterfile protein_collection

DESCRIPTION
  No_fasta is a script used to perform fasta searches on selected orfs in a 
  masterfile. No_fasta performs the following actions, in that order:

   1) Use mf2stad(1) to produce a coordinates file of all the genes in the
      masterfile, except the Vars, Sigs, Mots and Mobs. Be sure to use -o if
      the masterfile is not listed in genome_name.lst(1) (see FILES).

   2) Run flip to produce a prot.lst of all the orfs in the masterfile that have
      a length (without the stop codon) of at least 48. If -g was no used (see
      OPTIONS) no_fasta looks in genome_name.lst (see FILES) to get the genetic
      code number. If it finds one, it runs flip with the option -g <CodeFound>.
      Otherwise, flip is run without the -g switch (see flip's(1) manpage for a
      description of its behaviour in this case). Flip's behavior can be 
      configured with the -L switch (see OPTIONS).

   3) Use protfilt to filter the orfs: separate those for which there is at 
      least one gene in the coordinates file that overlaps the orf by a given 
      percentage (see -F) from those for which there is not. This will create
      the files prot.lst.nonoverlap and prot.lst.overlap in the current 
      directory.	
      
   4) Run bfasta on the orfs listed in prot.lst.nonoverlap. The results are
      written in bfasta.out, unless a different output file name was specified
      with -O (see OPTIONS). The behavior of bfasta can be customized with the
      switches -a and -s (see OPTIONS).

    
OPTIONS
   -o ocode
    Use ocode as the organism code to use when running mf2stad(1). This option
    must be used if the masterfile is not listed in genome_name.lst (see FILES).

   -g gcode
    Pass the option "-g gcode" to flip. Gcode must be a positive number not
    greater than 21 and not equal to 7 or 8. If -g is not used, no_fasta looks
    in genome_name.lst (see FILES) to get the genetic code number. If it finds
    one, it runs flip with the option -g <CodeFound>. Otherwise, flip is run
    without the -g switch (see flip's(1) manpage for a description of its
    behaviour in this case).

   -l length
    When running flip, pass the option -l length. By default flip is run with
    -l48.

   -F num
    When running protfilt, pass the option -F%o<num>-100. By default protfilt
    is run with the option -F%o20-100

   -s nb_scores
     Show nb_scores. This switch controls the behavior of bfasta(1). If this
     option is not used, 20 scores will be displayed.

   -a nb_align
     Show nb_align alignments per score. If this option is not used, 10 
     alignments per score will be displayed.

   -O outfile
     Write results in file outfile. By default, the results of no_fasta are
     written in file no_fasta.out

FILES
   /share/supported/apps/ogmp/lib/genome_names.lst
     Contains information on all the OGMP projects
  
DEPENDENCIES
   /share/supported/apps/ogmp/bin/mf2stad
     To create the coordinates file
   /share/supported/apps/ogmp/bin/flip  
     To produce prot.lst
   /share/supported/apps/ogmp/bin/protfilt
     To produce prot.lst.nonoverlap and prot.lst.overlap
   /share/supported/apps/ogmp/bin/bfasta
     To execute fasta searches on selected orfs

SEE ALSO
   mf2stad(1), bfasta(1), protfilt(1), flip(1)

AUTHOR
   Gertraud Burger (specs)
   Nicolas Brossard (design and programming)

Organelle Genome Megasequencing Project, Sept. 1998