Gapped permutation pattern discovery for gene order comparisons.

Full Abstract

The list of species whose complete DNA sequence have been read is growing steadily, and it is believed that comparative genomics is in its early days. Permutations patterns (groups of genes in some "close" proximity) on gene sequences of genomes across species is being studied under different models, to cope with this explosion of data. The challenge is to (intelligently and efficiently) analyze the genomes in the context of other genomes. In this paper, we present a generalized model that uses three notions, gapped permutation patterns (with gap g), genome clusters, via quorum, K>1, parameter, and, possible multiplicity in the patterns. The task is to automatically discover all permutation patterns (with possible multiplicity), that occur with gap g in at least K of the given m genomes. We present (log mN (I) + /Sigma/log/Sigma/N (O)) time algorithm where m is the number of sequences, each defined on Sigma, N (I) is the size of the input and N (O) is the size of the maximal gene clusters that appear in at least K of the m genomes.

Learn Faster Today Improve your study skills

Author information

Author/s: Parida, Laxmi (L);

Affiliation: Computational Biology Center, IBM T.J.Watson Research Center,Yorktown Heights, NewYork 10598, USA. parida(-atsign-)us.ibm.com

Journal and publication information

Publication Type: Journal Article

Journal: Journal of computational biology : a journal of computational molecular cell biology (J Comput Biol), published in United States. (Language: eng)

Reference: -2007 Jan-Feb; vol 14 (issue 1) : pp 45-55

Dates: Created 2007/03/26; Completed 2007/04/26;

PMID: 17381345, status: MEDLINE (last retrieval date: 12/26/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

External Links for this article (including full text providers, if available):

Click Electronic Full-text Provider Links to see options for finding the electronic full text links to this article. Note there may be a subscription or fee required for access to the full text. See our FAQ for information on finding FREE full text articles.

This article may also be located in paper journal collections available in many libraries. Use the Journal and Publication Information above to find the full article.

MeSH headings (categories)

This article was linked to the MESH Headings shown below.

These are the highest related articles currently in the database:

See 100+ related articles.