[Bioperl-l] need help urgently

[Chris Fields]

Neeti,

Something like this?

http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#esummary_-.3E_efetch

chris

On Sep 4, 2009, at 7:21 AM, Neeti Somaiya wrote:

> Thanks. Its an interesting tool.
>
> But I want to do this programatically.
>
> I have gene ids to start with. Cant find a method to directly get
> sequence with gene id as input. So using the method of getting
> sequence with accession as input, for which I need to know accessions
> for my gene ids first. Is this a right approach? Please guide me. My
> main aim is to get the nucleotide sequence of a gene from ids entrez
> gene id/gene name. PLease guide me. I am confused.
>
> -Neeti
> Even my blood says, B positive
>
>
>
> On Fri, Sep 4, 2009 at 5:35 PM, Emanuele Osimo<e.osimo at gmail.com>  
> wrote:
>> Try this:
>> http://david.abcc.ncifcrf.gov/conversion.jsp
>>
>> Emanuele
>>
>>
>> On Fri, Sep 4, 2009 at 12:13, Neeti Somaiya  
>> <neetisomaiya at gmail.com> wrote:
>>>
>>> Thanks for the replies.
>>>
>>> So the get seq by accession/GI worked for me. Now can anyone tell me
>>> the easiest way to get the GI /Accession of a gene from the gene
>>> id/gene name?
>>>
>>> -Neeti
>>> Even my blood says, B positive
>>>
>>>
>>>
>>> On Fri, Sep 4, 2009 at 2:47 PM, Neeti  
>>> Somaiya<neetisomaiya at gmail.com>
>>> wrote:
>>>> Thanks for the link.
>>>> So I need only the following lines of code to get the sequence?
>>>>
>>>> use Bio::DB::GenBank;
>>>> $db_obj = Bio::DB::GenBank->new;
>>>> $seq_obj = $db_obj->get_Seq_by_id(2);
>>>>
>>>> How do I print the sequence?
>>>> $seq_obj->seq ??
>>>>
>>>> -Neeti
>>>> Even my blood says, B positive
>>>>
>>>>
>>>>
>>>> On Fri, Sep 4, 2009 at 1:31 PM, K. Shameer<shameer at ncbs.res.in>  
>>>> wrote:
>>>>>
>>>>> Retrieving a sequence from a database : BioPerl HOWTO
>>>>> http://bit.ly/RWIot
>>>>>
>>>>> Trust this helps,
>>>>> Khader Shameer
>>>>> NCBS - TIFR
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I have an input list of gene names (can get gene ids from a  
>>>>>> local db
>>>>>> if required).
>>>>>> I need to fetch sequences of these genes. Can someone please  
>>>>>> guide me
>>>>>> as to how this can be done using perl/bioperl?
>>>>>>
>>>>>> Any help will be deeply appreciated.
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> -Neeti
>>>>>> Even my blood says, B positive
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
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