[Genome] BLAT minimum seq

[Ann Zweig]

Hello Vesko,

	Towards the bottom of the BLAT page, there is a brief explanation of 
the way it works:

BLAT on DNA is designed to quickly find sequences of 95% and greater 
similarity of length 25 bases or more. It may miss more divergent or 
shorter sequence alignments. It will find perfect sequence matches of 25 
bases, and sometimes find them down to 20 bases. BLAT on proteins finds 
sequences of 80% and greater similarity of length 20 amino acids or 
more. In practice DNA BLAT works well on primates, and protein blat on 
land vertebrates.

Also, please see the BLAT FAQs: http://genome.ucsc.edu/FAQ/FAQblat

And the BLAT User's Guide:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

	I hope this information is helpful to you.  Please don't hesitate to 
contact the mail list again if you require further assistance.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Vesselin Baev wrote:
> Dear all,
> If I blat query 100nt, what is the minimum lenth (default), that it can
> find..10,15,20..or?
> 
> Vesko
>