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Open Access Research

Similarity searches in genome-wide numerical data sets

Galina Glazko12, Michael Coleman1 and Arcady Mushegian13*

Author Affiliations

1 Stowers Institute for Medical Research, 1000 E 50th St., Kansas City MO 64110, USA

2 University of Rochester Medical Center, Rochester, NY 14642, USA

3 Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA

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Biology Direct 2006, 1:13  doi:10.1186/1745-6150-1-13

Published: 30 May 2006

Abstract

We present psi-square, a program for searching the space of gene vectors. The program starts with a gene vector, i.e., the set of measurements associated with a gene, and finds similar vectors, derives a probabilistic model of these vectors, then repeats search using this model as a query, and continues to update the model and search again, until convergence. When applied to three different pathway-discovery problems, psi-square was generally more sensitive and sometimes more specific than the ad hoc methods developed for solving each of these problems before.

Reviewers

This article was reviewed by King Jordan, Mikhail Gelfand, Nicolas Galtier and Sarah Teichmann.