[Genome] BLAT with 19mer

[Brooke Rhead]

Hi Archie,

One of our developers recommends the following:

----
  minimum for hit = 2*stepSize + TileSize -1
  2*5 + 10 - 1 = 19

So use stepSize = 5 with TilesSize=10.
This will increase the memory requirements a little.

Note that its not guaranteed to work with short mRNA
sequences with introns in them.
----

I hope this information helps.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

Russell, Archie wrote:
> Hi
> 
> What parameters should I give BLAT to find matches between sequence 19
> bases long and either mRNA or genomic sequence?
> 
> Thanks,
> Archie 
> 
> 
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