Question: Blast thresholds for orthologs search in bacteria
1
gravatar for ask
4.2 years ago by
ask10
ask10 wrote:

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?

blast bacteria orthologs • 2.1k views
ADD COMMENTlink modified 4.2 years ago by adrian.altenhoff520 • written 4.2 years ago by ask10
1
gravatar for adrian.altenhoff
4.2 years ago by
Switzerland
adrian.altenhoff520 wrote:

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)

ADD COMMENTlink written 4.2 years ago by adrian.altenhoff520
0
gravatar for dago
4.2 years ago by
dago2.5k
Germany
dago2.5k wrote:

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/

 

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by dago2.5k
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