NAME

     rlgs7.pl - split genome sequences into rlgs subsequences

SYNOPSIS

     rlgs7.pl [options] file1 [file2, ...]

DESCRIPTION

     rlgs7.pl is a program to split genome  sequences  into  rlgs
     subsequences  by cutting the sequences at enzyme restriction
     sites.  Files file1, file2,... contain genome  fasta  files.
     Sequences  are  split  at  three  enzyme  restriction sites.
     Subsequences which contain the restriction site of the first
     enzyme are output to a file in fasta fragment format.

OPTIONS

     -o <output_file>
          Output all subsequences to file  output_file.   Default
          is out.fff.

     -out_seq1 <seq1_file>
          Output first subsequences  to  file  seq1_file.   First
          subsequences are produced by splitting the sequences at
          the first two restriction sites.

     -out_seq2 <seq2_file>
          Output second subsequences to file  seq2_file.   Second
          subsequences are produced by splitting the sequences at
          all three restriction sites.

     -out_loc <loc_file>
          Output tab-delimited location file loc_file  containing
          the locations of the subsequences in the fasta files.

     -name1 <Restrictase1 name>
     -name2 <Restrictase2 name>
     -name3 <Restrictase3 name>
          Restriction enzyme names.  Defaults  for  name1,  name2
          and name3 are Not1, EcoRV and Hinf1.

     -site1 <Restrictase1 site>
     -site2 <Restrictase2 site>
     -site3 <Restrictase3 site>
          Restriction enzyme sites 1,  2,  and  3.   <Restrictase
          site>  is a string of <A,C,G,T,N> where N matches A, C,
          G or T.   Defaults  for  site1,  site2  and  site3  are
          GCGGCCGC, GATATC and GANTC, respectively.

     -no_header
     Don't print header line at beginning of file (default.)

     -header
     Don't print header line at beginning of file.

USAGE

     To create a tiff rlgs image from a set of fasta files  which
     are in the directory /usr/local/fasta enter:
     rlgs7.pl /usr/local/fasta/*.fa
     fff2cnm -gc out.fff vrlgs.cnm
     generate_RLGS vrlgs.cnm vrlgs.tif

     The tiff image will be stored in the file vrlgs.tif.

SEE ALSO

     generate_RLGS(1), edit_fff.pl(1), fff2cnm.pl(1)

ACKNOWLEDGEMENTS

     rlgs7.pl is a modification of a program rlgs.pl developed by
     Dr. Stanislav Volik and Dr. Joel Kirch at UCSF.

AUTHORS

     Joel Kirch, Stanislav Volik, Tahmina Ansari, Rephael Wenger

COPYRIGHT

     rlgs7.pl is distributed as is for non-commercial For commer-
     cial use, contact Dr. Volik or Dr. Kirch at UCSF.