BLAST search of primer sequence - (Jul/24/2008 )

Hi all,

I tried to interrogate primer sequences published in the articles by using BLAST2 to see where exactly the primer sequences are derived, and I often got the "No match" result, even it should match. I encountered this quite often, and I am quite puzzled. Any suggestions/comments?

Thanks very much.

Kenny1970

See the section "Search for short and near exact matches" under Nucleotide BLAST is useful for primer or short nucleotide motif searches here.

I used Nucleotide BLAST and successfully align all of the primer sequences on the genomic sequence. Thanks very much for that link, which is very helpful.

You can use these two tools to search primer hits on th genome:

Primer check: http://www.tigerteamconsulting.com/SpliceCenter/PrimerCheck
in silico PCR http://genome.ucsc.edu/cgi-bin/hgPcr?db=hg18