Blast thresholds for orthologs search in bacteria
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9.8 years ago
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Hi all!

I want to find orthologs which are present in all Streptococcus strains using blast and local db with protein sequences from these strains. Is there common approach to set thresholds on sequence identity and coverage?

orthologs blast bacteria • 3.6k views
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9.8 years ago

To find orthologs within a defined taxonomic range, you could use hierarchical orthologous groups (HOGs) on this level. Several orthology databases provide such groups, e.g. EggNOG, OrthoDB or OMA.

For species covered by OMA (our own inference method) you can get precomputed HOGs from the web, i.e. http://omabrowser.org/oma/hogs/ARGR_STRR6/Streptococcus/

For your own set of species of interest, you could use the OMA standalone package to compute HOGs (http://omabrowser.org/standalone)

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