%0 Journal Article %1 Hagopian2010SATCHMOJS %A Hagopian, Raffi %A Davidson, John R. %A Datta, Ruchira S. %A Samad, Bushra %A Jarvis, Glen R. %A Sjolander, Kimmen %D 2010 %J Nucl. Acids Res. %K phylogeny sequence-analysis software web-server %N suppl\_2 %P W29--34 %R 10.1093/nar/gkq298 %T SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction %U http://dx.doi.org/10.1093/nar/gkq298 %V 38 %X We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/. 10.1093/nar/gkq298

@article{Hagopian2010SATCHMOJS, abstract = {We present the jump-start simultaneous alignment and tree construction using hidden Markov models ({SATCHMO}-{JS}) web server for simultaneous estimation of protein multiple sequence alignments ({MSAs}) and phylogenetic trees. The server takes as input a set of sequences in {FASTA} format, and outputs a phylogenetic tree and {MSA}; these can be viewed online or downloaded from the website. {SATCHMO}-{JS} is an extension of the {SATCHMO} algorithm, and employs a divide-and-conquer strategy to jump-start {SATCHMO} at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all {HMM}-{HMM} scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the {PREFAB} benchmark dataset show that {SATCHMO}-{JS} provides a statistically significant improvement in alignment accuracy over {MUSCLE}, Multiple Alignment using Fast Fourier Transform ({MAFFT}), {ClustalW} and the original {SATCHMO} algorithm. The {SATCHMO}-{JS} webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/. 10.1093/nar/gkq298}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Hagopian, Raffi and Davidson, John R. and Datta, Ruchira S. and Samad, Bushra and Jarvis, Glen R. and Sjolander, Kimmen}, biburl = {https://www.bibsonomy.org/bibtex/21914d69c5abf2de2d2a1b32b892e794c/karthikraman}, citeulike-article-id = {7118119}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkq298}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl\_2/W29}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20430824}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20430824}, day = 1, doi = {10.1093/nar/gkq298}, interhash = {a389eebb86be88c08eaeb3cddd59a973}, intrahash = {1914d69c5abf2de2d2a1b32b892e794c}, journal = {Nucl. Acids Res.}, keywords = {phylogeny sequence-analysis software web-server}, month = jul, number = {suppl\_2}, pages = {W29--34}, pmid = {20430824}, posted-at = {2010-05-03 07:47:45}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {{SATCHMO}-{JS}: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction}, url = {http://dx.doi.org/10.1093/nar/gkq298}, volume = 38, year = 2010 }