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PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses
1Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, Via Celoria, 26, 20133 Milano, Italy. graziano.pesole@unimi.it
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/Pats earch.html.