GapMind

Automated annotation of amino acid biosynthesis | Abstract GapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea ( http: papers.genomics.lbl gov gaps ). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 seconds. To avoid error-prone “transitive” annotations, GapMind relies primarily on a database of experimentally-characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for “best hit” approaches. To improve GapMind’s coverage, we examined genetic data from 35 bacteria that grow in minimal media and we filled many gaps in amino acid biosynthesis pathways.

Webpage:
https://papers.genomics.lbl.gov/cgi-bin/gapView.cgi

Publications:

Tags:

small molecule molecular interactions, pathways and networks mobile genetic elements

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