Run Morgan Price's program, "Curated Blast", on a Genome in KBase.
Given a genome and a query, find characterized proteins whose descriptions match the query, and then search the genome for homologs of those proteins. You can use any Genome object. - This is the KBase wrapper for Curated BLAST -
For example, queries could be "perchlorate", "manganate". Genomes could be any Genome object, eg "Shewanella_amazonensis_SB2B".
Uses MMseqs2 to run BLAST searches.
Link to Curated Blast on Github
Related Publications
- Price MN, Arkin AP: Curated BLAST for Genomes. mSystems. 2019. DOI 10.1128/mSystems.00072-19 link: https://msystems.asm.org/content/4/2/e00072-19 Steinegger M and Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, 2017 doi: 10.1038/nbt.3988 link: https://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3988.html ,
App Specification:
https://github.com/OGalOz/curated_blast/tree/8a19a8ad23fad0840d7a3e3a4cf78833748d1e29/ui/narrative/methods/run_curated_blastModule Commit: 8a19a8ad23fad0840d7a3e3a4cf78833748d1e29