A toolset being developed for the Build a Cell project to interpret dependencies between genes and enable unit-testing of gene function in both existing and forward-engineered genomes. The near-term goal is to be abel to mine prokaryotic genome information from curated databases like Ecocyc and Kegg and provide ranked lists of candidate protospacers for CRISPRi knockdown (for unit-testing). The current version provides an interface with Ecocyc and extracts E. coli annotations to generate an output spreadsheet consisting of:
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Promoter ID
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Promoter orientation
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Sequence surrounding promoters (specifiable)
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Genes in each operon (one operon per promoter)
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Transcription unit ID (one or greater transcription units per promoter)
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Positive and negative strand protospacer candidates targeting the sequence surrounding promoters
##Current statistics 2152 annotated genes from E. coli integrated (out of expected 4377 in E. coli K-12)
3841 promoters (operons) from E. coli
7 protospacers identified per promoter region on average (searching from 60 bps upstream to 60 bps downstream of +1)
Simply download OrganismBreadBoard.09-a4 from https://github.com/EndyLab/Gene-Mining-Scripts.git or clone the project:
git clone https://github.com/sestaton/sesbio.git
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Fork it!
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Create your feature branch:
git checkout -b my-new-feature -
Commit your changes:
git commit -am 'Add some feature' -
Push to the branch:
git push origin my-new-feature -
Submit a pull request!
##Contact Email us at atg@buildacell.io! Website: https://www.buildacell.io