title: Identifying multiple alignment regions satisfying simple formulas and patterns.
abstract: BACKGROUND
  When studying multiple alignments of genomic sequences one frequently aims to locate and count regions which satisfy a set of constraints. These regions may be putatively functional, but researchers may also be interested in quantifying the frequency of occurrences of certain patterns.
  
  
  RESULTS
  We have developed a program that applies simple formulas and pattern specifications to multiple alignments, reporting the positions and counts of conforming regions. As an example, we have navigated a 15-species alignment of the CAV2-CAV1 region and outlined some findings regarding PPARgamma binding sites.
  
  
  BACKGROUND
  Our software and the accompanying documentation can be obtained at no charge by contacting the authors. It can also be accessed at http://ranger.uta.edu/~nick/compgen
authors.affiliation: Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA. nick@cse.uta.edu
authors.forename: Nikola
authors.initials: N
authors.lastname: Stojanovic
authors.forename: Ken
authors.initials: K
authors.lastname: Dewar
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D017124:Conserved Sequence; D005787:Gene Frequency; D047495:PPAR gamma / Q000235:genetics*; D010363:Pattern Recognition, Automated / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D047495:PPAR gamma