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

[Volkening, Jeremy]

 Phil,

I believe including the flag "-F F" on the command line (which will turn
off low-complexity filtering) should address your problem. Hope it
helps,

Jeremy


-----Original Message-----
From:
biodevelopers-bounces+jeremy.volkening=ars.usda.gov at bioinformatics.org
[mailto:biodevelopers-bounces+jeremy.volkening=ars.usda.gov at bioinformati
cs.org] On Behalf Of Phil Princely
Sent: Thursday, March 22, 2007 10:40 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
_______________________________________________
Biodevelopers mailing list
Biodevelopers at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/biodevelopers