Hi I want to pop this post up. Though this is not exactly my question but related. Actually I have few primer sequences, and I want to blast them to specific species strains.
My primer sequences looks like
And I want to check them against B.bifidum,
http://www.ncbi.nlm.nih.gov/nuccore/U25952.1
First as a newbie, I tried direct blastn agains blast formatted B.bifidum strain. But then realise in the primers there are many other letters as M,R,G besides A,T,C,G;
So no wonder I don’t get a direct match with blastn. Can anybody please suggest me how should I proceed.
Thanks a lot, Mitra
My primer sequences looks like
27Fmod
V1+V2+V3
AGRGTTTGATCMTGGCTCAG
ill519Rmod
V1+V2+V3
GTNTTACNGCGGCKGCTG
V1+V2+V3
AGRGTTTGATCMTGGCTCAG
ill519Rmod
V1+V2+V3
GTNTTACNGCGGCKGCTG
http://www.ncbi.nlm.nih.gov/nuccore/U25952.1
First as a newbie, I tried direct blastn agains blast formatted B.bifidum strain. But then realise in the primers there are many other letters as M,R,G besides A,T,C,G;
So no wonder I don’t get a direct match with blastn. Can anybody please suggest me how should I proceed.
Thanks a lot, Mitra
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