[BioSQL-l] getting exon information from genbank files

ankit soni ankitson at gmail.com
Sun Apr 10 14:04:03 EDT 2005


Hi all,
I have just started using BioSQL for one of my projects and I have
loaded few genbank files in the MySQL database using BioPerl and the
standard schema.
I wanted to ask how can I get the information about the exons, introns
from the database.
If I use the following querry I get the start and end position but I
am not able to find out what limits(start_pos and end-pos) stand for
i.e. gene or exon or intron.
mysql> select * from location where seqfeature_id='XXXX';
+-------------+---------------+-----------+---------+-----------+---------+--------+------+
| location_id | seqfeature_id | dbxref_id | term_id | start_pos |
end_pos | strand | rank |
+-------------+---------------+-----------+---------+-----------+---------+--------+------+
|       YYYY |         XXXX  |      NULL  |    NULL |      ABC  |   
EFG |      1    |    1     |
+-------------+---------------+-----------+---------+-----------+---------+--------+------+

It would be very helpful if somebody can guide me.
I am sorry if I am unable to use the correct biological terms as I
know very little of biology.

Ankit Soni
Junior Undergraduate
Dept. of Computer Science
IIT kanpur
India


More information about the BioSQL-l mailing list