Question: Online blast and standalone blast return different hits?
gravatar for ishengomae
6.3 years ago by
Tanzania, United Republic Of
ishengomae110 wrote:

Lately I have issues with blast. Anyway what I want to do could have different and easier process so I welcome any help. I have a list of cow protein sequences(many, about 200 sequences) and I want to identify their orthologs from about 50 vertebrate species. In the end I want to use these orthologs for an indepth evolutionary analysis. With online blast (specifically tblastn  against refseq_rna database), I can get a sensible species hits (evolutionarily). With standalone blast running it from a script, different species come out even with a stringent setting in terms of e-values. I don't want Plasmodium or Drosophila sequences to appear in my hits! Is there a way I can set my blast so as to return hits in the order similar to the web blast?

EDIT: Just to give an example, if I query blast with a single gene query, I would get the first hit being Bos taurus (cow) mRNA (which is what is expected), the second may be Bos mutus (Yak) followed by some other species in the ungulate or equiine families.  But with standalone blast, I dont get expected species in that order.

blast alignment • 1.9k views
ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by ishengomae110

I would look if the online and local blast databases, as well as parameters and blast versions equal first. Blast is so widely used, that such issue would surface fast, it seems like a local problem.

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Pavel Senin1.9k

Indeed I have 2.2.28+ version and I think the online version is up to 2.2. 29+ so I'll reinstall and see what happens. Thanks for attention.

ADD REPLYlink written 6.3 years ago by ishengomae110
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1414 users visited in the last hour