PatSearch: A pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance

Abstract

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 alogarithm 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 occurence through a Markov chain simulation. Results: The application of the proposed alogarithm 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.