Multiple structural alignment and clustering of RNA sequences | Zendy

Elfar Torarinsson | Zendy; Jakob H. Havgaard | Zendy; Jan Gorodkin | Zendy

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Multiple structural alignment and clustering of RNA sequences

Author(s) -

Elfar Torarinsson,

Jakob H. Havgaard,

Jan Gorodkin

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/btm049

Subject(s) - multiple sequence alignment , perl , sequence alignment , alignment free sequence analysis , computer science , structural alignment , similarity (geometry) , sequence (biology) , set (abstract data type) , scripting language , pairwise comparison , cluster analysis , smith–waterman algorithm , computational biology , artificial intelligence , biology , genetics , peptide sequence , programming language , gene , image (mathematics)

An apparent paradox in computational RNA structure prediction is that many methods, in advance, require a multiple alignment of a set of related sequences, when searching for a common structure between them. However, such a multiple alignment is hard to obtain even for few sequences with low sequence similarity without simultaneously folding and aligning them. Furthermore, it is of interest to conduct a multiple alignment of RNA sequence candidates found from searching as few as two genomic sequences.

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