View source for Vigor4

[[Category:Software]][[Category:Biology]][[Category:Annotation]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|vigor4}}
|{{#vardefine:url|https://github.com/JCVenterInstitute/VIGOR4}}
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<!--Description-->
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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.


<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


Check database directory for other available databases:
$ module load vigor4
$ ls $VIGOR_DB

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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* VIGOR_DB - database directory
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