[Bioperl-l] Clones and Unigene annotation
brian_osborne at cognia.com
Wed Jan 7 16:55:30 EST 2004
It sounds like part of your project may involve retrieving id's from Genbank
entries. Take a look at the Feature-Annotation HOWTO, perhaps it will answer
some of your questions on this particular topic. However this doesn't sound
like the tricky part of your project...
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Law, Annie
Sent: Wednesday, January 07, 2004 4:30 PM
To: 'bioperl-l at portal.open-bio.org'
Subject: [Bioperl-l] Clones and Unigene annotation
I have started to look at the resources available on the bioperl website.
It looks like there are
are some tools available that will help me accomplish my task.
I have a list of clone IDs and I would like to do some annotation. For
starters I have gone to
the I.M.A.G.E. site and I have found the Genbank accession numbers
corresponding to the clone IDs.
I would like to find the corresponding unigene IDs for these accession
My goal is to have a database with clone IDs, accession number, and unigene
ID, and allow a user to
add his own personal annotation as well. Later on, I would like to annotate
with other information
I would like to know if bioperl is the way to go or if there is already
One of the advantages with bioperl is that I will be able to control how
often the database gets updated.
This is a problem with some of the tools I have seen that are available on
Basically, I think that there are two tools that are available from bioperl
that are of use to me.
There is a file called load_seqdatabase.pl that will allow me to load a
unigene file into a biosql db.
Aside from the resource link listed below is there any more documentation or
examples available for the
use of this script?
There are also Unigene objects and a parsing tool Bio::Cluster::UniGene, and
I saw in a March 2003 post that someone was trying to do something along the
same lines without the database idea
using the unigene objects.
However, the major complaint was that it was too slow (I will be dealing
with 20 000 clone IDs at a time).
I was wondering if anything has changed since then. Even if the process was
My next question would be if I used the parser to find a matching accession
number and the corresponding
unigene ID would the next natural step be to insert this data in some
database I created.
I am not sure whether the load_seqdatabase.pl tool or the unigene objects is
best suited for my needs.
Since I am new to bioperl I am not to sure what the intention was for the
creation of the Unigene objects
and what most people use them for.
I would appreciate any tips on the most appropriate way to use bioperl to
accomplish my task.
thanks very much,
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