Difference between revisions of "Uproc"
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_LIB - library directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_INC - includes directory |
<!--Configuration--> | <!--Configuration--> | ||
Revision as of 21:29, 6 December 2019
Description
With rapidly increasing volumes of biological sequence data the functional analysis of new sequences in terms of similarities to known protein families challenges classical bioinformatics. The ultrafast protein classification (UProC) toolbox implements a novel algorithm ("Mosaic Matching") for large-scale sequence analysis and is now available in terms of an open source C library. UProC is up to three orders of magnitude faster than profile-based methods and achieved up to 80% higher sensitivity on unassembled short reads (100 bp) from simulated metagenomes. UProC does not depend on a multiple alignment of family-specific sequences. Therefore, in addition to the protein domain classfication according to the Pfam database, UProC can, in principle, also provide the detection of KEGG Orthologs. We provide a precompiled database for KEGG Ortholog classification which we applied to the prediction of functional repertoires from short reads.
Environment Modules
Run module spider uproc to find out what environment modules are available for this application.
System Variables
- HPC_UPROC_DIR - installation directory
- HPC_UPROC_BIN - executable directory
- HPC_UPROC_LIB - library directory
- HPC_UPROC_INC - includes directory