Protein database searches for multiple alignments.

• DOI: 10.1073/pnas.87.14.5509
• Publication Date: 2006-05-31T11:22:37Z
• Authors: S F Altschul; D J Lipman
• Keywords: Sequence (biology); Protein structure database; Alignment-free sequence analysis

Protein database searches frequently can reveal biologically significant sequence relationships useful in understanding structure and function. Weak but meaningful patterns be obscured, however, by other similarities due only to chance. By searching a for multiple as opposed pairwise alignments, distant are much more easily distinguished from background noise. Recent statistical results permit the power of this approach analyzed. Given typical query sequence, an algorithm described here permits current protein searched three-sequence alignments less than 4 min. Such have revealed variety subtle that search methods would unable detect.