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Multiple alignment by sequence annealing

Schwartz, Ariel S. and Pachter, Lior (2007) Multiple alignment by sequence annealing. Bioinformatics, 23 (2). e24-e29. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20170307-134453947

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Abstract

MOTIVATION: We introduce a novel approach to multiple alignment that is based on an algorithm for rapidly checking whether single matches are consistent with a partial multiple alignment. This leads to a sequence annealing algorithm, which is an incremental method for building multiple sequence alignments one match at a time. Our approach improves significantly on the standard progressive alignment approach to multiple alignment. RESULTS: The sequence annealing algorithm performs well on benchmark test sets of protein sequences. It is not only sensitive, but also specific, drastically reducing the number of incorrectly aligned residues in comparison to other programs. The method allows for adjustment of the sensitivity/specificity tradeoff and can be used to reliably identify homologous regions among protein sequences. AVAILABILITY: An implementation of the sequence annealing algorithm is available at http://bio.math.berkeley.edu/amap/


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/bioinformatics/btl311DOIArticle
https://academic.oup.com/bioinformatics/article/23/2/e24/202846/Multiple-alignment-by-sequence-annealingPublisherArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© The Author 2006. Published by Oxford University Press. Ariel Schwartz was supported by NSF grant EF 03-31494. Lior Pachter was supported by NIH grant R01HG2362 and NSF grant CCF0347992.
Funders:
Funding AgencyGrant Number
NSFEF-0331494
NIHR01HG2362
NSFCCF-0347992
Issue or Number:2
Record Number:CaltechAUTHORS:20170307-134453947
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170307-134453947
Official Citation:Ariel S. Schwartz, Lior Pachter; Multiple alignment by sequence annealing. Bioinformatics 2007; 23 (2): e24-e29. doi: 10.1093/bioinformatics/btl311
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74861
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:07 Mar 2017 22:08
Last Modified:24 Feb 2020 10:30

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