Question: Ideal settings for blasting a protein/cdna against a genome?
gravatar for cmdcolin
18 months ago by
United States
cmdcolin1.1k wrote:

Are there any ideal settings for BLAST to align a protein or cdna against a genome? Or is it perhaps even misleading to rely on BLAST this way and it's better to use something like exonerate (protein2genome/est2genome)?

blast exonerate • 744 views
ADD COMMENTlink written 18 months ago by cmdcolin1.1k

Ideal settings are context-dependent: are the proteins/cDNA from the same species as the reference genome, or from a somewhat distant species? What is your purpose, finding close homologs or even distant homologs?

edit: anyway, I would use Spaln or Exonerate for proteins, and GMAP or Spaln or Exonerate for cDNA.

ADD REPLYlink modified 18 months ago • written 18 months ago by h.mon23k

It would be same species or fairly closely related (e.g. getting a danio gene, blasting against fish of interest). I don't necessarily have exact use cases but there were biologists wanting to find the location of their gene of interest in a poorly annotated genome, and they had cdna sequences from either experiment or a closely related species, and they wanted to blast against it and then look at it in the genome browser. I just noticed when trying to help that blasting a cDNA against the genome would get lots of similar paralog hits but might not have been obtaining the top matches as the right gene (or sometimes it would not even be in list) using default BLASTN of a cdna to the genome

ADD REPLYlink written 18 months ago by cmdcolin1.1k

If that is the case, maybe the best approach is to iterate over blast algorithms: start with megablast; if nothing found, try dc-megablast; if nothing found, try blastn - of course, this is only feasible if done by hand with a few genes.

But the problem may be with the assembly, it may be too fragmented and the gene is not present or is fragmented between several contigs.

ADD REPLYlink written 18 months ago by h.mon23k
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