Commit 07e28536 authored by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz

Expanded Readme

parent 766696bb
# BiG-SCAPE
BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a Python script that calculates a distance matrix between groups of genes. In particular, BiG-SCAPE has been built with the aim of analyzing **Biosynthetic Gene Clusters**, which encode the pathways for Secondary Metabolites.
**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.
BiG-SCAPE works by predicting and comparing conserved domains found in the proteins encoded in the gene clusters.
As input, BiG-SCAPE takes GenBank files from the output of [antiSMASH](https://antismash.secondarymetabolites.org) with BGC predictions, as well as reference BGCs from the [MIBiG repository](https://mibig.secondarymetabolites.org/). 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](https://github.com/nselem/EvoDivMet).
This comparison allows to form a distance matrix that can be used to group similar BGCs automatically.
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.
Learn more about BiG-SCAPE in the [wiki](https://git.wageningenur.nl/medema-group/BiG-SCAPE/wikis/home).
![](BiG-SCAPE CORASON Workflow.png)
![BiG-SCAPE/CORASON workflow](BiG-SCAPE CORASON Workflow.png)
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