[Bioperl-l] need help urgently

[Neeti Somaiya]

Hi,

Thanks for your reply. I saw this before and wanted to try this, but I
am unable to install this module of EUtilities. When I search on CPAN,
it gives me the entire bioperl package in the download option of this
module. Can I not get a tar.gz file of this module alone, which I can
gzip, untar and then run the make and all to install it? I dont want
to install entire bioperl again as I am using an older version. Any
suggestions?

-Neeti
Even my blood says, B positive



On Fri, Sep 4, 2009 at 6:00 PM, Chris Fields<cjfields at illinois.edu> wrote:
> 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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>>>
>>>
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>
>