1BP_OLIGO_COUNT(1)     User Contributed Perl Documentation    BP_OLIGO_COUNT(1)
2
3
4

NAME

6       oligo_count - oligo count and frequency
7

SYNOPSIS

9         Usage:  oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
10                 [-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
11                 [-o/--out OUTFILE]
12

DESCRIPTION

14       This scripts counts occurrence and frequency for all oligonucleotides
15       of given length.
16
17       It can be used to determine what primers are useful for frequent
18       priming of nucleic acid for random labeling.
19
20       Note that this script could be run by utilizing the compseq program
21       which is part of EMBOSS.
22

OPTIONS

24       The default sequence format is fasta. If no outfile is given, the
25       results will be printed to standard out. All other options can entered
26       interactively.
27

FEEDBACK

29   Mailing Lists
30       User feedback is an integral part of the evolution of this and other
31       Bioperl modules. Send your comments and suggestions preferably to the
32       Bioperl mailing list.  Your participation is much appreciated.
33
34         bioperl-l@bioperl.org                  - General discussion
35         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
36
37   Reporting Bugs
38       Report bugs to the Bioperl bug tracking system to help us keep track of
39       the bugs and their resolution. Bug reports can be submitted via the
40       web:
41
42         http://bugzilla.open-bio.org/
43

AUTHOR - Charles C. Kim

45       Email cckim@stanford.edu
46

HISTORY

48       Written July 2, 2001
49
50       Submitted to bioperl scripts project 2001/08/06
51
52       >> 100 x speed optimization by Heikki Lehvaslaiho
53
54
55
56perl v5.12.0                      2010-04-29                 BP_OLIGO_COUNT(1)