Difference between revisions of "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. | 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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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{uc:{{#var:app}}}}_DIR | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{uc:{{#var:app}}}}_BIN | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| + | * HPC_{{uc:{{#var:app}}}}_REF - reference datasets directory | ||
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Latest revision as of 20:09, 12 August 2022
Description
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.
Environment Modules
Run module spider hamstr to find out what environment modules are available for this application.
System Variables
- HPC_HAMSTR_DIR - installation directory
- HPC_HAMSTR_BIN - executable directory
- HPC_HAMSTR_REF - reference datasets directory