>I need some help in searching through the sequence data bases for splice
>I am trying to look at sequences next to splice junctions
>but in the EXON.
M. Gouy has developped a database named ACNUC that allows such request (ref).
A RETRIEVAL SYSTEM FOR GENBANK, EMBL, AND NBRF/PIR
ACNUC is a retrieval system for the nucleotide sequence databases GenBank
or EMBL and for the protein sequence data base NBRF/PIR.
ACNUC allows to select sequences from many criteria (keyword, taxonomy, bibliography,
sequence length, molecule type, organelle etc...) from these 3 data
bases, to translate protein-coding genes in protein, and to extract
selected sequences in user files. ACNUC is unique in providing direct access
to coding regions (e.g. protein coding regions, tRNA or rRNA coding regions)
of DNA fragments present in GenBank and in EMBL (introns, exon, CDS, 3'UTR, mRNA,
5'UTR, tRNA, etc... described on the FEATURES).
Notably, ACNUC allows to extract fragments adjacent to the extremities of a
subsequence (CDS, intron, tRNA, exon, etc...). Therefore it is possible to
systematically extract, for example, 50 nt downstream of introns end of human
protein encoding genes (or according to any other criteria).
ACNUC is known to run on Sun (SunOs or Solaris), IBM Risc workstations,
SGI computers, Dec-alpha systems, and VAX/VMS systems.
It should be easily installed on most unix platforms. Contact M. Gouy for help
for other unix systems.
ACNUC is distributed by anonymous ftp from the internet address:
biom3.univ-lyon1.fr or, numerically, 126.96.36.199
The directory there is /pub/acnuc
ref: M. Gouy et al. (1985) CABIOS 3:167-172
M. Gouy et al. (1984) Nucl. Acids Res. 12:121-127
Contact = M. Gouy: mgouy at evomol.univ-lyon1.fr
Laboratoire de Biometrie, Genetique et Biologie des Populations
URA CNRS 243 Universite Claude Bernard - Lyon I
43, Bd du 11 Novembre 1918 F-69622 Villeurbanne cedex
Tel: +33 188.8.131.52
E-mail: duret at biomserv.univ-lyon1.fr