[Bioperl-l] need help urgently

[Neeti Somaiya]

I actually want the nucleotide sequence of the gene. I thought the
Bio::DB::EntrezGene would give me a seq_obj for an entrez gene id and
then the seq method on that $seq_obj->seq() will give me the actual
genomic nucleotide sequence of the gene. But this doesnt happen. I am
able to print gene symbol using $seq_obj->display_id and able to do
other things, but I wanted the gene nucleotide sequence.

-Neeti
Even my blood says, B positive



On Tue, Sep 8, 2009 at 1:56 AM, Smithies,
Russell<Russell.Smithies at agresearch.co.nz> wrote:
> This example code from the wiki _definitely_ works:
> http://bio.perl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_Bio::DB::EntrezGene_to_get_genomic_coordinates
> =========================================
>
> use strict;
> use Bio::DB::EntrezGene;
>
> my $id = shift or die "Id?\n"; # use a Gene id
>
> my $db = new Bio::DB::EntrezGene;
> $db->verbose(1); ###
>
> my $seq = $db->get_Seq_by_id($id);
>
> my $ac = $seq->annotation;
>
> for my $ann ($ac->get_Annotations('dblink')) {
>        if ($ann->database eq "Evidence Viewer") {
>                # get the sequence identifier, the start, and the stop
>                my ($contig,$from,$to) = $ann->url =~
>                  /contig=([^&]+).+from=(\d+)&to=(\d+)/;
>                print "$contig\t$from\t$to\n";
>        }
> }
>
> ======================================
>
> So if it doesn't work for you, there are a few things you need to check:
> * what version of BioPerl are you using?
> * are you behind a firewall?
> * are you using a proxy?
> * do you need to submit username/password for either of the 2 above
> * turn on 'verbose' messages, it may help you debug
>
>
> If you're still having problems, get back to me and I'll see if I can help.
>
> --Russell
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Neeti Somaiya
>> Sent: Monday, 7 September 2009 10:04 p.m.
>> To: Emanuele Osimo; bioperl-l
>> Subject: Re: [Bioperl-l] need help urgently
>>
>> I tried using EntrezGene instead of GenBank, as is given in the link
>> that you sent :
>>
>> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_datab
>> ase
>>
>> http://doc.bioperl.org/releases/bioperl-current/bioperl-
>> live/Bio/DB/EntrezGene.html
>>
>> use Bio::DB::EntrezGene;
>>
>>     my $db = Bio::DB::EntrezGene->new;
>>
>>     my $seq = $db->get_Seq_by_id(2); # Gene id
>>
>>     # or ...
>>
>>     my $seqio = $db->get_Stream_by_id([2, 4693, 3064]); # Gene ids
>>     while ( my $seq = $seqio->next_seq ) {
>>           print "id is ", $seq->display_id, "\n";
>>     }
>>
>> This doesnt seem to work.
>>
>>
>> -Neeti
>> Even my blood says, B positive
>>
>>
>>
>> On Fri, Sep 4, 2009 at 1:09 PM, Emanuele Osimo<e.osimo at gmail.com> wrote:
>> > Hello,
>> > have you tried this?
>> >
>> http://bio.perl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_Bio::DB::GenBan
>> k_when_you_have_genomic_coordinates
>> >
>> > Emanuele
>> >
>> > On Fri, Sep 4, 2009 at 08:49, Neeti Somaiya <neetisomaiya at gmail.com> wrote:
>> >>
>> >> 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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>> Bioperl-l at lists.open-bio.org
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