BiG-SCAPE: Difference between revisions
Moskalenko (talk | contribs) m Text replacement - "#uppercase" to "uc" |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Category:Software]][[Category:Phylogenetics]] | [[Category:Software]][[Category:Phylogenetics]][[Category:Biology]][[Category:Phylogenetics]][[Category:Pipeline]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|bigscape}} | |{{#vardefine:app|bigscape}} | ||
Revision as of 12:52, 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