https://github.com/mfcovington/provean-assembly-line

Find amino acid substitutions from SNPs and run PROVEAN to estimate functional severity
https://github.com/mfcovington/provean-assembly-line

Last synced: over 1 year ago
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Find amino acid substitutions from SNPs and run PROVEAN to estimate functional severity

• Host: GitHub
• URL: https://github.com/mfcovington/provean-assembly-line
• Owner: mfcovington
• Created: 2015-01-16T07:46:38.000Z (over 11 years ago)
• Default Branch: develop
• Last Pushed: 2016-09-09T23:44:45.000Z (almost 10 years ago)
• Last Synced: 2025-03-20T14:40:27.371Z (over 1 year ago)
• Language: Perl
• Homepage:
• Size: 45.9 KB
• Stars: 5
• Watchers: 1
• Forks: 4
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
### Find amino acid substitutions

Use `find-aa-substitutions.pl` to identify amino acid substitutions.

Requirements:

- SNP files

- GFF3 file

- Genomic FASTA reference file

### Run PROVEAN

Use `run-provean.pl` to determine the putative functional severity of the amino acid changes.

Requirements:

- Amino acid substitution files

- CDS FASTA reference file

- PROVEAN installation

### Filter PROVEAN results

Use `filter-provean-results.pl` to filter PROVEAN results for a single gene, a file containing a list of genes, or all genes within a genomic range.

*Version 0.4.0*