PatSearch: a Pattern Matcher Software That Finds Functional Elements in Nucleotide and Protein Sequences and Assesses Their Statistical Significance

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.