Finding Lincrna Alignments With Blast Versus Blat

Question

[Eric]

Hello,

I have a lincRNA sequence (XLOC) that I retrieved from the Broad Institute. When I BLAT the sequence against the human genome, I get a 100% match and it aligns with the correlating transcript (TCONS). However, when I BLAST the alignment, I get "No significant similarity found". Can anyone suggest why this might be?

Thanks.

[Nicolas Rosewick]

could you please put the blast parameter you used ?

[Eric]

database: Genome (all assemblies scaffolds). I've tried both megablast and blastn.

Answer 1

[Istvan Albert]

Make sure to disable the low complexity filter. It is on by default (sadly!) and that probably causes untold amounts of misleading results.

[Eric]

Still nothing happening. But thanks for the tip.