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 Inparanoid-Database. Ortholog groups of genes are then formed from the pairwise Inparanoid ortholog assignments applying the criterion of transitive closure. Based on these ortholog groups, hidden markov models are generated using the HMMER package, each representative of a single cluster of orthologous genes on the chosen set of reference taxa (Details). For each HMM, 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 here for details on the workflow.

Click here to see an example output .

HaMStR is now also available as a standalone version. You can download the hamstrsearch_local package together with several core-ortholog sets from the download directory.