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


bp_oligo_count - oligo count and frequency


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


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.


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.


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AUTHOR - Charles C. Kim



Written July 2, 2001

Submitted to bioperl scripts project 2001/08/06

>> 100 x speed optimization by Heikki Lehvaslaiho

2021-08-15 perl v5.32.1