bp_mutate(1p) [debian man page]

BP_MUTATE(1p)						User Contributed Perl Documentation					     BP_MUTATE(1p)

NAME

       mutate.pl - randomly mutagenize a single protein or DNA sequence

SYNOPSIS

	 ./mutate.pl -p 25 -i test.fa -n 5 -f swiss -o muts.swiss

	 #or

	 ./mutate.pl --percent=25 --input=test.fa --number=5 -output=x.fa

DESCRIPTION

       Randomly mutagenize a single protein or DNA sequence one or more times.	Specify percentage mutated and number of resulting mutant
       sequences.  Print mutagenized sequences to STDOUT or write to an output file.

	 -h|--help    Help
	 -p|--percent Percent mutagenized
	 -n|--number  Number of mutant sequences created
	 -o|--output  Output file (optional)
	 -f|--format  Output format (default: fasta)
	 -i|--input   Input file

FEEDBACK

       User feedback is an integral part of the evolution of this and other Bioperl scripts. Send your comments and suggestions to the Bioperl
       mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Brian Osborne, bosborne at alum.mit.edu

perl v5.14.2							    2012-03-02							     BP_MUTATE(1p)

BP_AACOMP(1p)						User Contributed Perl Documentation					     BP_AACOMP(1p)

NAME

       aacomp - amino acid composition of protein sequences

SYNOPSIS

	 aacomp [-f/--format FORMAT] [-h/--help] filename
	 or
	 aacomp [-f/--format FORMAT] < filename
	 or
	 aacomp [-f/--format FORMAT] -i filename

DESCRIPTION

       This scripts prints out the count of amino acids over all protein sequences from the input file.

OPTIONS

       The default sequence format is fasta.

       The sequence input can be provided using any of the three methods:

       unnamed argument
	    aacomp filename

       named argument
	    aacomp -i filename

       standard input
	    aacomp < filename

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

HISTORY

       Based on aacomp.c from an old version of EMBOSS

perl v5.14.2							    2012-03-02							     BP_AACOMP(1p)