[BiO BB] On searching Refseq_mrna database

[Boris Steipe]

Dear Anonymous,
The point of these searches is to retrieve matches that might not be recognizable after conceptual translation because of frameshifts or gene-model errors in query and/or subject. For this reason, you would not search m-RNA in six frames to begin with, but you would use genomic DNA (or preliminary datasets from genome sequencing assemblies).

Best,
Boris


On 2011-02-04, at 1:51 PM, Skull Crossbones wrote:

> I wish to do a tblastx search against the Refseq_mrna database. However I'm sceptical about searching the database in all six reading frames.For protein coding mRNAs will it be more appropriate to search the database in frame 1 only? as the mrna sequence will correspond to the protein coding region.
> 
> Thanks in advance 
> 
> 
> 
> 
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