Multiple alignment by sequence annealing Export

@article{citeulike:1068491, 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/ Contact: sariel@cs.berkeley.edu 10.1093/bioinformatics/btl311}, author = {Schwartz and Pachter, Lior}, citeulike-article-id = {1068491}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btl311}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/23/2/e24.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/23/2/e24.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/2/e24}, citeulike-linkout-4 = {http://www.ingentaconnect.com/content/oup/cabios/2007/00000023/00000002/e24}, citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/17237099}, citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=17237099}, day = {15}, doi = {10.1093/bioinformatics/btl311}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {alignment, annealing, multiple, sequence}, month = {January}, number = {2}, pages = {e24--29}, posted-at = {2008-11-20 13:46:21}, priority = {2}, publisher = {Oxford University Press}, title = {Multiple alignment by sequence annealing}, url = {http://dx.doi.org/10.1093/bioinformatics/btl311}, volume = {23}, year = {2007} }

TY - JOUR ID - citeulike:1068491 L3 - citeulike-article-id:1068491 N2 - 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/ Contact: sariel@cs.berkeley.edu 10.1093/bioinformatics/btl311 IS - 2 JF - Bioinformatics SN - 1367-4803 EP - 29 TI - Multiple alignment by sequence annealing PB - Oxford University Press VL - 23 SP - e24 KW - alignment KW - annealing KW - multiple KW - sequence AU - Schwartz AU - Pachter, Lior PY - 2007/01/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btl311 ER -