ARCS

An aggregated related column scoring scheme for aligned sequences

Bin Song, Guangyu Chen, Jacek Szymanski, Guo Qiang Zhang, Anthony K H Tung, Jaewoo Kang, Sun Kim, Jiong Yang

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Motivation: 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 s coring 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.

Original languageEnglish
Pages (from-to)2326-2332
Number of pages7
JournalBioinformatics
Volume22
Issue number19
DOIs
Publication statusPublished - 2006 Oct 1

Fingerprint

Scoring
Consensus Sequence
Entropy
Proteins
Coring
Protein Sequence
Similarity Measure
Experimental Evaluation
Alignment

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Song, B., Chen, G., Szymanski, J., Zhang, G. Q., Tung, A. K. H., Kang, J., ... Yang, J. (2006). ARCS: An aggregated related column scoring scheme for aligned sequences. Bioinformatics, 22(19), 2326-2332. https://doi.org/10.1093/bioinformatics/btl398

ARCS : An aggregated related column scoring scheme for aligned sequences. / Song, Bin; Chen, Guangyu; Szymanski, Jacek; Zhang, Guo Qiang; Tung, Anthony K H; Kang, Jaewoo; Kim, Sun; Yang, Jiong.

In: Bioinformatics, Vol. 22, No. 19, 01.10.2006, p. 2326-2332.

Research output: Contribution to journalArticle

Song, B, Chen, G, Szymanski, J, Zhang, GQ, Tung, AKH, Kang, J, Kim, S & Yang, J 2006, 'ARCS: An aggregated related column scoring scheme for aligned sequences', Bioinformatics, vol. 22, no. 19, pp. 2326-2332. https://doi.org/10.1093/bioinformatics/btl398
Song, Bin ; Chen, Guangyu ; Szymanski, Jacek ; Zhang, Guo Qiang ; Tung, Anthony K H ; Kang, Jaewoo ; Kim, Sun ; Yang, Jiong. / ARCS : An aggregated related column scoring scheme for aligned sequences. In: Bioinformatics. 2006 ; Vol. 22, No. 19. pp. 2326-2332.
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