[Genome] BLAT Search Question

[Archana Thakkapallayil]

Hello Emmanuel,

Our web-based BLAT could process up to 25 sequences in one batch. If you 
would like to process more sequences, you should download the 
stand-alone BLAT. See this answer to a previous mail list question that 
gives more information on running batch query:

http://www.soe.ucsc.edu/pipermail/genome/2006-December/012454.html

Also, it is not possible to filter out the best hit when using the 
online BLAT.  Please see this previously answered mail list question 
that gives information on filtering out the best hit from the output 
using the stand-alone BLAT:

http://www.cse.ucsc.edu/pipermail/genome/2006-March/009918.html

I hope that this helps you. Please let us know if you have further 
questions.

Regards,

Archana
UCSC Genome Bioinformatics Group


Emmanuel Kamberov wrote:
> Hi, we are trying to create a custom annotation track from BLAT search
> output.  We have a few hundred short genomic DNA sequences (80-150 bp
> long).  How many sequences can be processed in one batch ?  Is there a
> way to filter only the highest scorring match for each sequence  when
> creating a PSL output file ?  
>  
> Thanks,
>  
> Emmanuel Kamberov
>  
> _____________________________________
>  
> Emmanuel Kamberov, Ph.D.
> Senior Research Scientist
> Rubicon Genomics, Inc.
> 4370 Varsity Drive,
> Ann Arbor, MI 48103
> Office:    734-677-2894
> Mobile:   734-274-1102
> kamberov at rubicongenomics.com <mailto:kamberov at rubicongenomics.com> 
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