[Bioperl-l] getting DNA sequence for exon features from GFF

kanmani radha kanmaninradha at gmail.com
Thu Aug 26 18:04:20 EDT 2010

HI, I made some progress since then....
- Installing  Bio::DB::DBI::mysql needed Biosql.

- Downloaded and installed biosql follow the instruction as given in their
- Created biosql db in my mysql server
- loaded schema using script from biosql

- installed DBI
- Now, I have problem with DBD::mysql. That reminds me couple years back i
had to struggle installing this driver on another machine. I thought i ask
around this time.

It fails with a bunch of error messages.....the first of it being....
dbdimp.h:22:49 error: mysql.h no such filer or directory

But, My mysql installation has header file in
"/usr/include/mysql3/mysql/mysql.h". Can anyone suggest how to move forward
from that.....


On Thu, Aug 26, 2010 at 2:24 PM, kanmani radha <kanmaninradha at gmail.com>wrote:

> Hi Chris and others,
> For a brief amount time i could get away using Bio::DB::Fasta to index
> fasta files and Bio::Tools::GFF to iterate thru GFF features. But, i hit the
> wall again. Looks like sequential access of GFF featuers is not sufficient,
> I want to have a random access to it. I see the only way to do that is by
> using Bio::DB::GFF as suggested by Chris.
> Here is my question. Is there any tutorial to configure Bioperl  or this
> module in particular to work with MySQL/postgres. I will really appreciate
> it.
> And thanks for all your help.
> Kanmani
> On Thu, Aug 26, 2010 at 10:08 AM, Chris Fields <cjfields at illinois.edu>wrote:
>> On Aug 26, 2010, at 11:22 AM, kanmani radha wrote:
>> > Hi Everyone,
>> >
>> > Thanks very much for this clarification.  Thanks a ton for every one who
>> > spared their time to educate me.
>> >
>> > I see your points.  Please correct me if I am wrong.
>> >
>> > I understand that, Its better to use use Bio::DB::SeqFeature or
>> Bio::DB::GFF
>> > to load the fasta sequences (from a separate multifasta) file and
>> > then Bio::Tools::GFF to parse the feature info from a gff file . Then
>> query
>> > the created database for the relevent GFF coordinates....
>> >
>> > I will implement this.
>> >
>> > Thanks once again.
>> > Kanmani
>> Yes, in general.  I forgot to mention that you can have an in-memory
>> database as well, but it's only suggested if you have a few thousand or so
>> features and small sequences (I think bacterial chromosomes will work).
>> chris

More information about the Bioperl-l mailing list