pfw

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 multiple 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 generated by GCG programs or by readseq (checksums are ignored) or in MSA format as produced by psa2msa(1). If '-' is specified 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 integers 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 representation. J. Mol. Biol. 216:813-818.

SEE ALSO

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

AUTHOR

The pftools package was developed by Philipp Bucher. Any comments or suggestions should be addressed to <[email protected]>.