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CLAGen: a tool for clustering and annotating gene sequences using a suffix tree algorithm.

Sang il Han·Sung Gun Lee·Kyung-Hoon Kim·Chung Jung Choi·Young Han Kim·Kyu Suk Hwang
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Abstract

Most multiple gene sequence alignment methods rely on conventions regarding the score of a multiple alignment in pairwise fashion. Therefore, as the number of sequences increases, the runtime of sequencing expands exponentially. In order to solve the problem, this paper presents a multiple sequence alignment method using a linear-time suffix tree algorithm to cluster similar sequences at one time without pairwise alignment. After searching for common subsequences, cross-matching common subsequences were generated, and sometimes inexact matching was found. So, a procedure aimed at masking the inexact cross-matching pairs was suggested here. In addition, BLAST was combined with a clustering tool in order to annotate the clusters generated by suffix tree clustering. The proposed method for clustering and annotating genes consists of the following steps: (1) construction of a suffix tree; (2) searching and overlapping common subsequences; (3) grouping subsequence pairs; (4) masking cross-matching pairs; (5) clustering gene sequences; (6) annotating gene clusters by the BLAST search. The performance of the proposed system, CLAGen, was successfully evaluated with 42 gene sequences in a TCA cycle (a citrate cycle) of bacteria. The system generated 11 clusters and found the longest subsequences of each cluster, which are biologically significant.

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AlgorithmsArtificial IntelligenceBase SequenceChromosome MappingDocumentationMolecular Sequence DataMultigene FamilyPattern Recognition, AutomatedSequence AlignmentSequence Analysis, DNASoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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Sang il Han, Sung Gun Lee, Kyung-Hoon Kim, Chung Jung Choi, Young Han Kim, Kyu Suk Hwang. 2005-12-27. CLAGen: a tool for clustering and annotating gene sequences using a suffix tree algorithm.. https://doi.org/10.1016/j.biosystems.2005.11.001

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