unBLASTable sequence?

Andrew Dalke dalke at bioreason.com
Tue Aug 3 22:13:17 EST 1999


Paraic Kenny <paraic at icr.ac.uk> said:
> I was trying to BLAST a protein sequence today at the NCBI blast
> server and in the results, part of my query sequence came up as a
> row of XXXXXXXXs even though it is directly identical to a sequence
> in the databases.

See http://www.ncbi.nlm.nih.gov/BLAST/filtered.html .

Redo your search and untoggle the filtering checkbox.  By default
the NCBI BLAST searchs mask out regions of low complexity.  I
imagine other sites do so as well.

						Andrew Dalke
						dalke at bioreason.com




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