Multiple alignment by aligning alignments | Zendy

Travis J. Wheeler | Zendy; John Kececioglu | Zendy

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Multiple alignment by aligning alignments

Author(s) -

Travis J. Wheeler,

John Kececioglu

Publication year - 2007

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btm226

Subject(s) - multiple sequence alignment , merge (version control) , computer science , oracle , benchmark (surveying) , weighting , consistency (knowledge bases) , algorithm , sequence alignment , data mining , artificial intelligence , information retrieval , medicine , biochemistry , chemistry , software engineering , geodesy , radiology , peptide sequence , gene , geography

Multiple sequence alignment is a fundamental task in bioinformatics. Current tools typically form an initial alignment by merging subalignments, and then polish this alignment by repeated splitting and merging of subalignments to obtain an improved final alignment. In general this form-and-polish strategy consists of several stages, and a profusion of methods have been tried at every stage. We carefully investigate: (1) how to utilize a new algorithm for aligning alignments that optimally solves the common subproblem of merging subalignments, and (2) what is the best choice of method for each stage to obtain the highest quality alignment.

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