title: PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  A Web interface is available at: http://bigarea.area.ba.cnr.it:8000/EmbIT/Pats earch.html.
authors.affiliation: Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, Via Celoria, 26, 20133 Milano, Italy. graziano.pesole@unimi.it
authors.forename: G
authors.initials: G
authors.lastname: Pesole
authors.forename: S
authors.initials: S
authors.lastname: Liuni
authors.forename: M
authors.initials: M
authors.lastname: D'Souza
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000235:genetics; D016208:Databases, Factual; D006657:Histones / Q000235:genetics; D006801:Humans; D009690:Nucleic Acid Conformation; D010363:Pattern Recognition, Automated; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D006657:Histones; D012333:RNA, Messenger; D004247:DNA