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Finding Lincrna Alignments With Blast Versus Blat

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
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updated by Istvan Albert Istvan Albert • written by Eric • Eric

could you please put the blast parameter you used ?

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written by Nicolas Rosewick Nicolas Rosewick

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

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written by Eric • Eric

1 answer

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

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written by Istvan Albert Istvan Albert

Still nothing happening. But thanks for the tip.

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written by Eric • Eric

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