title: SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules.
abstract: CONCLUSIONS
  Functional modules within protein sequences are often extracted by consensus sequence patterns representing a linear motif; however, other functional regions may only be described by combined features such as amino acid composition, profiles of amino acid properties and randomly distributed short sequence motifs. If only a small number of functional examples are well characterized, the researcher needs a tool to extract similar sequences for further investigation.
  
  
  METHODS
  We provide the web application 'SAPA tool', which allows the user to search with combined properties, ranks the extracted target regions by an integrated score, estimates false discovery rates by using decoy sequences and provides them as a sequence file or spreadsheet. Source code, user manual and the web application implemented in Perl, HTML, CSS and JavaScript and running on Apache are freely available at http://sapa-tool.uio.no/sapa/
authors.affiliation: IStLS, 78727 Oberndorf, Germany, Engelhardt Institute of Molecular Biology, Moscow 119991, Russia, Department of Molecular Biosciences, Glyconor Mass Spectrometry, University of Oslo, 0316 Oslo and Norbrain Mass Spectrometry Facility, Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway.
authors.forename: Josef
authors.initials: J
authors.lastname: Maier
authors.forename: Alexei A
authors.initials: AA
authors.lastname: Adzhubei
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Egge-Jacobsen
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis*; D020407:Internet; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D000596:Amino Acids; D011506:Proteins