title: ARCS: an aggregated related column scoring scheme for aligned sequences.
abstract: BACKGROUND
  Biologists frequently align multiple biological sequences to determine consensus sequences and/or search for predominant residues and conserved regions. Particularly, determining conserved regions in an alignment is one of the most important activities. Since protein sequences are often several-hundred residues or longer, it is difficult to distinguish biologically important conserved regions (motifs or domains) from others. The widely used tools, Logos, Al2co, Confind, and the entropy-based method, often fail to highlight such regions. Thus a computational tool that can highlight biologically important regions accurately will be highly desired.
  
  
  RESULTS
  This paper presents a new scoring scheme ARCS (Aggregated Related Column Score) for aligned biological sequences. ARCS method considers not only the traditional character similarity measure but also column correlation. In an extensive experimental evaluation using 533 PROSITE patterns, ARCS is able to highlight the motif regions with up to 77.7% accuracy corresponding to the top three peaks.
  
  
  BACKGROUND
  The source code is available on http://bio.informatics.indiana.edu/projects/arcs and http://goldengate.case.edu/projects/arcs
authors.affiliation: Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Song
authors.forename: Jeong-Hyeon
authors.initials: JH
authors.lastname: Choi
authors.forename: Guangyu
authors.initials: G
authors.lastname: Chen
authors.forename: Jacek
authors.initials: J
authors.lastname: Szymanski
authors.forename: Guo-Qiang
authors.initials: GQ
authors.lastname: Zhang
authors.forename: Anthony K H
authors.initials: AK
authors.lastname: Tung
authors.forename: Jaewoo
authors.initials: J
authors.lastname: Kang
authors.forename: Sun
authors.initials: S
authors.lastname: Kim
authors.forename: Jiong
authors.initials: J
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins