How to search small sequences? - (Nov/17/2009 )

Hi Everyone..!
I want to search whether a particular inverted repeat sequence present in the promoter region of E.coli gene is also present in other species of bacteria. Since it is just a 20bp long region, I dont know how to use NCBI blast option sad.gif guide me pls rolleyes.gif . I thank all of you..

Abhay

-DNAlooper-

You can read this guide from NCBI http://blast.ncbi.nlm.nih.gov/Blast.cgi?CM..._TYPE=FAQ#Short

Basically, you need to set a high value for "expect", turn off filter, and set a small window size.

-pcrman-

pcrman on Nov 18 2009, 12:02 PM said:

You can read this guide from NCBI http://blast.ncbi.nlm.nih.gov/Blast.cgi?CM..._TYPE=FAQ#Short

Basically, you need to set a high value for "expect", turn off filter, and set a small window size.

Thank you very much for timely reply. I shall go through.

-DNAlooper-