Re: Blast - exact same sequence only gives 98%

Hi Phil,

That is probably due to filtering- to get 100% just turn off the filter.

Marty

On 3/23/07, Phil Princely <[email protected]> wrote:
> Hi all,
>
> I'm new here, so sorry if this is a bit of an obvious question. I've
> been using blast for a while now, but am still learning. Here's my
> problem:
>
> I used formatdb to make a blast database from a text file with about
> 2000 genes. Everything went well, and I could query the database. But
> when I input a sequence from the original text file, the result isn't
> always 100%. Sometimes it comes out 98% or 95%, when it should always
> be 100%. When I look at the results, I find one or more series of xs,
> signifying a missing part of data. For example:
>
> Score = 1815 bits (4702), Expect = 0.0
>  Identities = 913/953 (95%), Positives = 913/953 (95%)
>
> LTLDRLSNTLSGGESQRISLATQXXXXXXXXXXXXDEPSIGLHQ (Query)
> LTLDRLSNTLSGGESQRISLATQ            DEPSIGLHQ
> LTLDRLSNTLSGGESQRISLATQLGSSLVGSLYVLDEPSIGLHQ (Subject)
>
> Is there a way to make this 100%. I want to run the 2000 genes against
> another genome to find 100% similar regions, 95% similar regions and
> so on.
>
> Thanks
>
> Phil P
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-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS334
775-784-7042
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