BiG-SCAPE: Difference between revisions
Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|bigscape}} |{{#vardefine:url|https://git.wageningenur.nl/medema-group/BiG-SC..." |
No edit summary |
||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
[[Category:Software]][[Category:Phylogenetics]] | [[Category:Software]][[Category:Phylogenetics]][[Category:Biology]][[Category:Genomics]][[Category:Pipeline]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|bigscape}} | |{{#vardefine:app|bigscape}} | ||
| Line 28: | Line 28: | ||
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 | ||
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 12:53, 15 August 2022
Description
BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.
As input, BiG-SCAPE takes GenBank files from the output of antiSMASH with BGC predictions, as well as reference BGCs from the MIBiG repository. As output, BiG-SCAPE generates tab-delimited output files, as well as a rich HTML visualization that includes multi-locus phylogenies of each Gene Cluster Family made using CORASON.
In principle, BiG-SCAPE can also be used on any other gene clusters, such as pathogenicity islands, secretion system-encoding gene clusters, or even whole viral genomes.
Environment Modules
Run module spider bigscape to find out what environment modules are available for this application.
System Variables
- HPC_BIGSCAPE_DIR - installation directory
- HPC_BIGSCAPE_BIN - executable directory