BLAT algorithm

[Sameen Ahmed]

Hello,

 

I am writing to ask whether the BLAT algorithm has changed at all in the past year. I BLAT’d a 20 mer sequence to hg38 recently, that previously BLAT found to be specific to one region.

Now, I see two hits.

 

Thanks,

Sameen

[Brian Lee]

Dear Sameen,

Thank you for using the UCSC Genome Browser and your question about changes to BLAT.

There have been changes in the recent past to expand the underlying genome represented by hg38 to include patches.

You can read more about these changes in this news update and blog post that emphasizes the changes:
http://genome.ucsc.edu/goldenPath/newsarch.html#030519
http://genome.ucsc.edu/blog/patches/#changes

While all the regions that you previously searched are still there in the underlying genome, new patch and fix sequences have been added in hg38 which means that BLAT and In-Silico PCR can find additional hits, which are likely on _alt and _fix sequences. Here is also more information about these new hits:
http://genome.ucsc.edu/FAQ/FAQblat.html#blat1c

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

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Brian Lee

UCSC Genome Browser  

UC Santa Cruz Genomics Institute |  Revealing life’s code.

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