Blast thresholds for orthologs search in bacteria

Question

[ask]

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?

Answer 1

[Adrian Altenhoff]

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)

Answer 2

[dago]

A few links that could help you to find the best solution:

• What Is The Best Method To Find Orthologous Genes Of A Species?
• http://paperity.org/p/41921187/choosing-blast-options-for-better-detection-of-orthologs-as-reciprocal-best-hits

You can also take a look at this program that I found really good: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837814/