Svar: RE: [Bioperl-l] blasting two identical seq yields only 88% identity

Anders Stegmann anst at
Sun Dec 25 14:41:04 EST 2005

All of you thanks for replying!

Because I am using Bio::Tools::Run::StandAloneBlast inside a script (I mised this in my mail) I can't change -F by going -F F. I found out that in order to change -F->F I just had to give the @params an extra F=>'F' argument. -F=>'F' won't work inside the @params though, but you got me on the right track.


>>> "Joseph Bedell" <jbedell at> 25-12-05 17:12 >>>
Hi Anders,

What you are seeing is probably low complexity filtering. By default,
NCBI-BLAST filters for low complexity sequence (the X's that you see in
the alignments). To turn it off, you need to specify -F F on the command


>-----Original Message-----
>From: bioperl-l-bounces at [mailto:bioperl-l-
>bounces at] On Behalf Of Anders Stegmann
>Sent: Sunday, December 25, 2005 2:58 AM
>To: bioperl-l at
>Subject: [Bioperl-l] blasting two identical seq yields only 88%
>Merry christmas BioPerl!
>I obtained some odd result blasting a protein sequence against
>a chromosome I new encoded the protein using tblastn.
>So I tested the problem by blasting the protein against a database only
>containing the exact same protein sequence using blastp (both files
>fasta formated).
>I obtained an identity of only 88% instead of 100%? A lot of X'ses were
>incorporated in the query sequence.
>I figured that it had something to do with the database formatting so I
>tried several possibilities with no luck
>(First I tried: formatdb -i SSD1pDB.txt -p T -o F).
>I have had this problem before blasting nucleotides.
>What can I do about it?
>Regards Anders.
>Bioperl-l mailing list
>Bioperl-l at

Bioperl-l mailing list
Bioperl-l at

More information about the Bioperl-l mailing list