[BiO BB] Extracting upstream sequence of a gene

[Paulo Nuin]

Hi Kiran

Try this
http://genome.ucsc.edu/cgi-bin/hgTables

IT is the tables browser. You can set several different parameters and 
do a search with hundreds of gene ids. Another option is to write a 
script and search for genes using the GeneSorter, but then you would 
need to parse the output.

HTH

Paulo



kannaiah at bsd.uchicago.edu wrote:
> Hi Paulo,
>
> I didnt really see a way to do multiple search on the genome browser.
> To extract from a certain region, i guess then i will have to compile the start
> and end regions of the gene in the chromosomes before hand?
>
> -Kiran
>
> Quoting Paulo Nuin <pnuin at terra.com.br>:
>
>   
>> Hi
>>
>> If you have the IDs of these genes you can do that on the UCSC genome 
>> browser. You can set a region to download automatically from a multiple 
>> search.
>>
>> Regards
>>
>> Paulo
>>
>>
>> kannaiah at bsd.uchicago.edu wrote:
>>     
>>> Hello,
>>>
>>> I have seen a few posts asking similar questions. I am looking to do
>>>       
>> something
>>     
>>> similar too. 
>>>
>>> I want to extract the upstream sequence of genes (upto 3000bp upstream)
>>>       
>> in
>>     
>>> Human. But going thru the ensembl website is ok, if one has few genes.
>>>
>>> But i have a few hundred genes. I was wondering what would be the best way
>>>       
>> to
>>     
>>> automate this.
>>> Should i try blasting the gene sequences to the Human Chromosome files, and
>>>       
>> then
>>     
>>> parse the blast output to get the position of the genes, and go back and
>>>       
>> read
>>     
>>> the chromosome sequence where it was found and get the upstream sequence.
>>>
>>> That would be a long way, hopefully there is someother shorter way to do
>>>       
>> this,
>>     
>>> which i am not aware of.
>>> Any suggestions would be welcome:)
>>>
>>> Thank you
>>>
>>> -hak
>>>
>>>
>>>
>>>
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