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
