Bioinformatics Vol. 16 no. 5 2000
Pages 439-450
© 2000 Oxford University Press
PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
1 Dipartimento di Fisiologia e Biochimica
Generali, Universitàdi Milano, Via
Celoria, 26, 20133 Milano, Italy
2 Centro di Studio sui Mitocondri e
Metabolismo Energetico del Consiglio Nazionale delle Ricerche, Via
Orabona, 4, 70126 Bari, Italy
3 Argonne National Laboratory, Mathematics
and Computer Science Division, 9700 South Cass Avenue Argonne,
Illinois 60439-4844, USA
Received on September 1, 1999
; revised on November 24, 1999
; accepted on November 24, 1999
Motivation: The identification of sequence patterns involved in gene regulation and expression is a major challenge in molecular biology. In this paper we describe a novel algorithm and the software for searching nucleotide and protein sequences for complex nucleotide patterns including potential secondary structure elements, also allowing for mismatches/mispairings below a user-fixed threshold, and assessing the statistical significance of their occurrence through a Markov chain simulation.
Results: The application of the proposed algorithm allowed the identification of some functional elements, such as the Iron Responsive Element, the Histone stem-loop structure and the Selenocysteine Insertion Sequence, located in the mRNA untranslated regions of post-transcriptionally regulated genes with the assessment of sensitivity and selectivity of the searching method.
Availability: A Web interface is available at: http://bigarea.area.ba.cnr.it:8000/EmbIT/Patsearch.html.
Contact: graziano.pesole{at}unimi.it
* To whom correspondence should be addressed.
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