[Biodevelopers] Blast - exact same sequence only gives 98%

[Ethan Strauss]

You need to turn off the filtering. I don't know the command off the top of my head, but it shouldn't be hard to find. 
Ethan

-----Original Message-----
From: biodevelopers-bounces+ethan.strauss=promega.com at bioinformatics.org on behalf of Phil Princely
Sent: Thu 3/22/2007 9:40 PM
To: biodevelopers at bioinformatics.org
Subject: [Biodevelopers] Blast - exact same sequence only gives 98%
 
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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