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Bioinformatics Advance Access published online on September 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti039
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 4, 2004
Revised August 2, 2004
Accepted August 23, 2004

Article

RAP: a new computer program for de novo identification of repeated sequences in whole genomes

Davide Campagna 1, Chiara Romualdi 1, Nicola Vitulo 1, Micky Del Favero 1, Matej Lexa 1, Nicola Cannata 1, and Giorgio Valle 1*

1 CRIBI, Università degli Studi di Padova, via Ugo Bassi 58b, I-35121 Padova, Italy

* To whom correspondence should be addressed. E-mail: giorgio.valle{at}unipd.it.


  Abstract

Motivation: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design. Several efficient algorithms based on word counting are available, but too short words decrease specificity while long words decrease sensitivity, particularly in degenerated repeats.

Results: The Repeat Analysis Program (RAP) is based on a new word-counting algorithm optimized for high resolution repeat identification using gapped words. Many different overlapping gapped words can be counted at the same genomic position, thus producing a better signal than the single ungapped word. This results in better specificity both in terms of low-frequency detection, being able to identify sequences repeated only once, and highly divergent detection, producing a generally high score in most intron sequences.

Availability: The program is freely available for non-profit organization, upon request to the authors.

Supplementary information: The program has been tested on the C. elegans genome using word lengths of 12, 14 and 16 bases. The full analysis has been implemented in the UCSC Genome Browser and is accessible at http://genome.cribi.unipd.it.


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