Question: Finding Lincrna Alignments With Blast Versus Blat
0
gravatar for Eric
6.6 years ago by
Eric90
Eric90 wrote:

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.

blast blat • 1.7k views
ADD COMMENTlink modified 6.6 years ago by Istvan Albert ♦♦ 81k • written 6.6 years ago by Eric90

could you please put the blast parameter you used ?

ADD REPLYlink written 6.6 years ago by Nicolas Rosewick8.3k

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

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Eric90
0
gravatar for Istvan Albert
6.6 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

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

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Istvan Albert ♦♦ 81k

Still nothing happening. But thanks for the tip.

ADD REPLYlink written 6.6 years ago by Eric90
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