Difference between revisions of "Vigor4"
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| − | + | <b>Annotatable Viruses</b> | |
| + | Vigor4 uses the VIGOR_DB project which currently has databases for the following viruses (code - database name): | ||
| − | + | * entovirus - Enterovirus | |
| + | * flua - Influenza A (human, avian, and swine) | ||
| + | * flub - Influenza B (human, avian, and swine) | ||
| + | * fluc - Influenza C (human) | ||
| + | * rtva - Rotavirus A | ||
| + | * rtvb - Rotavirus B | ||
| + | * rtvc - Rotavirus C | ||
| + | * rtvf - Rotavirus F | ||
| + | * rtvg - Rotavirus G | ||
| + | * sapo - Sapovirus | ||
| + | * sarscov2 - SARS-CoV-2 | ||
| + | * wnvI - West Nile Virus, Lineage I | ||
| + | * wnvII - West Nile Virus, Lineage II | ||
| + | * zikv - Zika Virus | ||
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| − | + | Check database directory for other available databases: | |
| − | + | $ module load vigor4 | |
| − | + | $ ls $VIGOR_DB | |
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<!--Modules--> | <!--Modules--> | ||
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * VIGOR_DB - database directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 14:25, 6 September 2024
Description
VIGOR4 (Viral Genome ORF Reader) is a Java application to predict protein sequences encoded in viral genomes. VIGOR4 determines the protein coding sequences by sequence similarity searching against curated viral protein databases.
Annotatable Viruses
Vigor4 uses the VIGOR_DB project which currently has databases for the following viruses (code - database name):
- entovirus - Enterovirus
- flua - Influenza A (human, avian, and swine)
- flub - Influenza B (human, avian, and swine)
- fluc - Influenza C (human)
- rtva - Rotavirus A
- rtvb - Rotavirus B
- rtvc - Rotavirus C
- rtvf - Rotavirus F
- rtvg - Rotavirus G
- sapo - Sapovirus
- sarscov2 - SARS-CoV-2
- wnvI - West Nile Virus, Lineage I
- wnvII - West Nile Virus, Lineage II
- zikv - Zika Virus
Check database directory for other available databases:
$ module load vigor4
$ ls $VIGOR_DB
Environment Modules
Run module spider vigor4 to find out what environment modules are available for this application.
System Variables
- HPC_VIGOR4_DIR - installation directory
- HPC_VIGOR4_BIN - executable directory
- VIGOR_DB - database directory