Hi Tar,
To answer your first question, yes, there is a way to make a batch DNA
sequence query. The Table Browser is a useful tool for doing this. From
main page, click on "Tables" on the top blue navigation bar. After
selecting a clade, genome, and assembly of your choice, set the following:
group: Genes and Gene Prediction Tracks
track: choose a gene prediction track you would like to use (I'll use
'UCSC Genes' for this example)
table: the default table will be the primary table for that track
('knownGene' in this case)
region: click on 'define regions', then paste in or upload a file with
your coordinates, click 'submit'
output format: sequence
output file: enter a file name to save your results to a file, or leave
blank to display results in the browser
Click 'get output'. On the following page, select 'genomic' then click
'get output'. Select any additional options, then click 'get sequence'.
For more information on how to use the Table Browser, please refer to
our help pages: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
For your second question, there is a utility for batch PCR queries
located in the kent source tree. You can download in silico PCR (isPCR)
and other utilities here: http://www.soe.ucsc.edu/~kent/exe/. If you run
'isPCR' without any arguments, you will see the usage statement.
I hope this information is useful and answers your questions. Feel free
to contact us again at [email protected] if you have any additional
questions.
Regards,
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On 10/5/2011 1:56 AM, Tar Viturawong wrote:
> Hello,
>
> I'm wondering whether there is a way to make
>
> 1) a batch genomic DNA sequence query (supplying multiple genome coordinates
> simultaneously)
> 2) a batch *in silico* PCR query (supplying multiple primer pairs
> simultaneously)
>
> without having to actually download the whole genome?
>
> Many thanks for your help!
>
> Tar
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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