title: SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.
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/.
authors.affiliation: Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
authors.forename: Raffi
authors.initials: R
authors.lastname: Hagopian
authors.forename: John R
authors.initials: JR
authors.lastname: Davidson
authors.forename: Ruchira S
authors.initials: RS
authors.lastname: Datta
authors.forename: Bushra
authors.initials: B
authors.lastname: Samad
authors.forename: Glen R
authors.initials: GR
authors.lastname: Jarvis
authors.forename: Kimmen
authors.initials: K
authors.lastname: Sjölander
mesh_terms: D000465:Algorithms; D020407:Internet; D008390:Markov Chains; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software