[Bioperl-l] Re: grouping sequences by DNA-binding domains -- elaboration

[Brian Osborne]

Olena,

I'm pretty sure that there's no code in Bioperl that accesses or parses CDD,
hopefully I'm corrected if I'm wrong.

Brian O.


On 10/18/05 2:26 PM, "Olena Morozova" <olenka.m at gmail.com> wrote:

> Hi Brian,
> 
> Thank you for your reply. It is the CDD (Conserved Domain Database) on
> the NCBI web site.
> Olena
> 
> On 10/18/05, Brian Osborne <brian_osborne at cognia.com> wrote:
>> Olena,
>> 
>> What database contains the information you're looking for?
>> 
>> Brian O.
>> 
>> 
>> On 10/16/05 8:17 PM, "Olena Morozova" <olenka.m at gmail.com> wrote:
>> 
>>> Hi agian,
>>> 
>>> I just figured out how to obtain a list of conserved domains for a
>>> given sequence using the SeqHound.pm module available at
>>> http://www.blueprint.org/seqhound/apifunctslist.html
>>> 
>>> Now I have a list of conserved domains for a given sequence and I need
>>> to extract information as to what these domains are and which ones are
>>> DNA-binding. Any help on this will be greatly appreciated
>>> 
>>> Thanks again,
>>> Olena
>>> 
>>> 
>>> On 10/16/05, Olena Morozova <olenka.m at gmail.com> wrote:
>>>> I have a list of transcription factor sequences, and I need to group
>>>> them according to the DNA-binding domains based on the classification
>>>> by TRANSFAC or any other database. Basically, I just need to extract
>>>> the DNA-binding domain information for a particular TF from a database
>>>> like TRANSFAC (I don't know what other databases would have this
>>>> information, but any will do) Anyone has any idea how to do this?
>>>> Thank you very much for your help and time
>>>> 
>>>> Olena
>>>> 
>>> 
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>> 
>> 
>>