[Genome] BLAT with 19mer

[Russell, Archie]

Thanks Brook,

I'm still not getting matches even though I have a 100% match between
the 19mer and the target mRNA.

Do you think I need to use the minScore/minMatch params?

Archie 

-----Original Message-----
From: Brooke Rhead [mailto:rhead at soe.ucsc.edu] 
Sent: Wednesday, July 11, 2007 1:43 PM
To: Russell, Archie
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] BLAT with 19mer

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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