Relay-Version: ANU News - V6.2.0 06/23/97 OpenVMS AXP V6.2; site chasm
Subject: Re: exon intron
Message-ID: <stevet.1237777540A at news.wsu.edu>
From: stevet at wsu.edu (Steve Thompson)
Date: Fri, 13 Feb 98 17:11:40 GMT
Reply-To: thompson at ribozyme.vadms.wsu.edu
References: <6bvg6m$2hg at net.bio.net>
Organization: Washington State University VADMS Center
X-Newsreader: VersaTerm Link v1.1.3
Hi all - regarding the following thread:
In Article <6bvg6m$2hg at net.bio.net>, Arlin Stoltzfus <arlin at is.dal.ca> wrote:
>Pierre Pontarotti wrote:
>>>> Hello I am looking for a data base that show all the genes for which the
>> exon intron organization is known
>> . . . .
>>It would be very useful for databases to have obligatory
>designations like "complete/partial" and "genomic/other".
Using NCBI's Entrez (at least the network version) one can search for the
term "biomol genomic" using the field "Properties" in the nucleotide
databases. This is guaranteed to find ONLY those sequences that are from
genomic DNA, not mRNA/cDNA. Of course you still gotta look at the entry to
see the exon/intron structure, if it has one, but at least you're not
wasting time looking through inappropriate cDNA entries. Naturally one can
further restrict this list to any other desired level, such as all genomic
sequences from mammals or all genomic sequences of some particular gene, etc.
I am a avid user and proponent of NEntrez - "try it you'll like it!"
However, sometimes the server does have problems and the taxonomy indices
have been corrupted for the last few weeks (even though I did complain to
NCBI about them) and the new advanced search function in version 6+ is a lot
less friendly than the old "More Booleans" window . . . .
Cheers - Steve
Steven M. Thompson
Consultant in Molecular Genetics and Sequence Analysis
Visualization, Analysis & Design in the Molecular Sciences (VADMS)
Washington State University, Pullman, WA 99164-4660, USA
AT&Tnet: (509) 335-3179 FAX: (509) 335-9688
INTERnet: thompson at ribozyme.vadms.wsu.edu