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 > > > > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
