[Bioperl-l] need help urgently

[Neeti Somaiya]

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
>> >>> _______________________________________________
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>> >>> Bioperl-l at lists.open-bio.org
>> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >>>
>> >>
>> >>
>> >>
>> >
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>
>