https://github.com/robsyme/genemark-extractor

Tools for taking GeneMark output and pulling out the relevant sequences from the original fasta file.
https://github.com/robsyme/genemark-extractor

Last synced: 24 days ago
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Tools for taking GeneMark output and pulling out the relevant sequences from the original fasta file.

• Host: GitHub
• URL: https://github.com/robsyme/genemark-extractor
• Owner: robsyme
• Created: 2010-03-01T01:30:15.000Z (over 14 years ago)
• Default Branch: master
• Last Pushed: 2010-03-09T00:46:18.000Z (over 14 years ago)
• Last Synced: 2023-04-10T14:49:16.043Z (over 1 year ago)
• Language: Ruby
• Homepage:
• Size: 74.2 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README

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README

        
Problem:

GeneMark will predict genes and output their locations in a gtf2 file.

We want two convert this into a gff3 format file.

It would also be nice to have a tool that pulls out the relevant sequences from the original fasta file.

A full gff3 format description can be found here: http://www.sequenceontology.org/gff3.shtml

There is a gff3 validator at: http://dev.wormbase.org/db/validate_gff3/validate_gff3_online

It is important that the gff file retains information about start and stop sites.

We want to know which gene models are complete so that we can qualify any secretion peptide predictions.