View source for HaMStR

[[Category:Software]][[Category:Biology]][[Category:Genomics]]
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|{{#vardefine:url|http://www.deep-phylogeny.org/hamstr/}}
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HaMSTR is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes. A-priori knowledge about orthology-relationships among genes in different sets of reference species is extracted from the [http://inparanoid.sbc.su.se/ Inparanoid-Database]. Ortholog groups of genes are then formed from the pairwise Inparanoid ortholog assignments applying the criterion of [http://www.deep-phylogeny.org/hamstr/images/tc.png transitive closure]. Based on these ortholog groups, hidden markov models are generated using the [[HMMER3|HMMER package]], each representative of a single cluster of orthologous genes on the chosen set of reference taxa (Details). For each HMM, [http://www.clccell.com/ hmmersearch_cell] is used to scan the translated EST-compilation for significant hits. Putative orthologs are then identified by re-blasting the candidate ESTs against a reference proteome. EST-sequences with the reference-protein as best BLAST hit that was used for the HMM-geneneration are returned as operational orthologs. Click [http://www.deep-phylogeny.org/hamstr/images/hamstr.png here] for details on the workflow.
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