[Genome] BLAT question

[Archana Thakkapallayil]

Hello Sam,

Here is the response from one of our developers to your question:

If you are trying to find nearby homologs, you could get a list of Known 
Gene sequences using our Table Browser, that are within the specified 
region of mouse chr7. Then take those sequences and run a batch BLAT job 
on them. You could even make a database that consisted just of the dna 
for the region and then search just that.

More information on using the Table Browser is here:
http://genome.cse.ucsc.edu/goldenPath/help/hgTablesHelp.html

If you are interested in distant homologs, then you might need to use BLAST.

I hope that this helps you. If this does not answer you question, please 
don't hesitate to write back to the list.

Regards,

--
Archana
UCSC Genome Bioinformatics Group


Sam, Judy wrote:
> I have just used BLAT for the first time, and discovered several nearly
> identical sequences to my query sequence within ~200 kb.  This "cluster" of
> related sequences would not have been otherwisse observable, since only my
> query sequence was a recognized gene.  Is there any way of generating a list
> of genes that are recently duplicated in this way, for example, all such
> genes on mouse Chr 7 between 65 and 84 Mb?
>
> Thank you for your help.
>
> Judy Sam
> City of Hope
> Duarte, CA 91010
>
>
> email: jsam at coh.org
> Tel. 626-301-8241
>
> "EMF <COH.org>" made the following annotations.
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