NAME


     pfw - weight sequences of a multiple sequence alignment





SYNOPSIS


     pfw       [  -hm ] [ -N shuffles ] [ -R seed ] [ -W weight ]

               [ -X gap_excision ] [ ms_file | - ] [ parameters ]





DESCRIPTION


     pfw  computes new weights for individual sequences in a mul-

     tiple sequence alignment using the  method  of  Sibbald  and

     Argos  (1990).   The  file  containing the multiple sequence

     alignment ('ms_file') must be either in MSF format as gener-

     ated  by  GCG programs or by readseq (checksums are ignored)

     or in MSA format as produced by psa2msa(1).  If '-' is spec-

     ified instead of a filename, the multiple sequence alignment

     is read from the standard input.  pfw writes a new  multiple

     sequence  alignment  with  modified weights in either MSF or

     MSA format to the standard output.





OPTIONS


     ms_file

          Input multiple sequence alignment file.

          This file contains a  multiple  sequence  alignment  in

          either  MSF  (default)  or MSA format. If the format is

          MSA, pfw will include the new weight of  each  sequence

          in  the  FASTA header using the xpsa(5) keyword weight.

          It will thus replace any existing weight=value pair  in

          the header line.  If the filename is replaced by a '-',

          pfw will read the multiple alignment from stdin.



     -h   Display usage help text.



     -m   Input multiple sequence alignment is in MSA format.



     -N shuffles

          Number of shuffles per sequence to be performed.

          Note that an average relative precision of r percent is

          achieved by approximately (100/r)-squared shuffles.

          Type: integer

          Default: 100 (10% precision)



     -R seed

          Seed for the random number generator.

          This must be a negative integer (zero or positive inte-

          gers will be reset to negative integers).

          Type: integer

          Default: -123456789



     -W weight

          Total weight.

          The initially computed weights will be multiplied by  a

          constant factor such that the sum of all weights equals

          this value.

          Default: 1



     -X gap_excision

          Gap excision threshold.

          This is the minimal fraction of  non-gap  characters  a

          column  of the multiple sequence alignment must contain

          in order to be considered for weighting.

          Default: 0.5





PARAMETERS


     Note:

          for backwards compatibility, release 2.3 of the pftools

          package  will  parse  the version 2.2 style parameters,

          but these are deprecated and the  corresponding  option

          (refer  to the options section) should be used instead.



     N=#  Shuffles per sequence.

          Use option -N instead.



     R=#  Random number seed.

          Use option -R instead.



     W=#  Total weight.

          Use option -W instead.



     X=#  Gap excision threshold.

          Use option -X instead.





EXIT CODE


     On successful completion of its task,  pfw  will  return  an

     exit  code  of  0.  If an error occurs, a diagnostic message

     will be output on standard error and the exit code  will  be

     different  from  0. When conflicting options where passed to

     the program but the task could  nevertheless  be  completed,

     warnings will be issued on standard error.





REFERENCES


     Sibbald  PR & Argos P. (1990).  Weighting aligned protein or

     nucleic acid sequences to correct  for  unequal  representa-

     tion.  J. Mol. Biol.  216:813-818.





SEE ALSO


     psa2msa(1), psa(5), xpsa(5)





AUTHOR


     The pftools package was developped by Philipp Bucher.

     Any   comments   or   suggestions  should  be  addressed  to

     <pftools@isb-sib.ch>.