SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction

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 phy...

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Bibliographic Details
Published in:	Nucleic acids research Vol. 38; no. Web Server issue; pp. W29 - W34
Main Authors:	Hagopian, Raffi, Davidson, John R, Datta, Ruchira S, Samad, Bushra, Jarvis, Glen R, Sjölander, Kimmen
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01-07-2010
Subjects:	Algorithms Internet Markov Chains Phylogeny Protein Structure, Tertiary Sequence Alignment - methods Sequence Analysis, Protein Software
Online Access:	Get full text
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Summary:	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/.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
ISSN:	0305-1048 1362-4962 1362-4962
DOI:	10.1093/nar/gkq298