aligning promoter regions to find a binding site - (Oct/16/2008 )

Hi everyone,

I have purified a transcription factor and have observed a band shift with a promoter region for a gene in Staphylococcus as well as its homologue in a different species. Is there a way that I could align the 2 probes to attempt to identify the binding site?

Any ideas much appreciated

hello bench buddy,

after you have sequenced your bands you can perform a blast2seq from ncbi. just go to this page and paste your sequences

http://blast.ncbi.nlm.nih.gov/bl2seq/wblast2.cgi

cheers.

Thanks toejam,

will give that a go.

Much appreciated.