Sequence-genome alignment - (May/28/2010 )

Hi everyone:

I have obtain two primer sequences of a promoter zone from a paper, but I am not sure that they are correct. I would like to align their sequences with human genome but I am not sure which is the better way. Is it correct to use BLASTn? Can anyone give me some advice about the way to proceed?

Thanks you very much

i think blast will be definitely a good choice! ...for bacteria thats the way i would do it ...and since the human genome is sequenced several times it should be no problem at all!

Regards,
p

If you want to aling your primer sequences to genome, UCSC in silico is a good tool to use http://genome.ucsc.edu/cgi-bin/hgPcr?db=hg19