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How to search small sequences?


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#1 DNAlooper

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Posted 17 November 2009 - 08:00 PM

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

"Support Bacteria, they are the only cultures some people have"


#2 pcrman

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Posted 17 November 2009 - 10:32 PM

You can read this guide from NCBI http://blast.ncbi.nl..._TYPE=FAQ#Short

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

#3 DNAlooper

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Posted 17 November 2009 - 11:50 PM

You can read this guide from NCBI http://blast.ncbi.nl..._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.

"Support Bacteria, they are the only cultures some people have"





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