bp_gccalc(1p) [debian man page]

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

NAME

       gccalc - GC content of nucleotide sequences

SYNOPSIS

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

DESCRIPTION

       This scripts prints out the GC content for every nucleotide sequence 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
	    gccalc filename

       named argument
	    gccalc -i filename

       standard input
	    gccalc < 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 script code (see bottom) submitted by cckim@stanford.edu

       Submitted as part of bioperl script project 2001/08/06

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

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

NAME

       oligo_count - oligo count and frequency

SYNOPSIS

	 Usage:  oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
		 [-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
		 [-o/--out OUTFILE]

DESCRIPTION

       This scripts counts occurrence and frequency for all oligonucleotides of given length.

       It can be used to determine what primers are useful for frequent priming of nucleic acid for random labeling.

       Note that this script could be run by utilizing the compseq program which is part of EMBOSS.

OPTIONS

       The default sequence format is fasta. If no outfile is given, the results will be printed to standard out. All other options can entered
       interactively.

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 - Charles C. Kim
       Email cckim@stanford.edu

HISTORY

       Written July 2, 2001

       Submitted to bioperl scripts project 2001/08/06

       >> 100 x speed optimization by Heikki Lehvaslaiho

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