Bioinformatics Vol. 17 no. 8 2001
Pages 671-675
© 2001 Oxford University Press
Generation of a database containing discordant intron positions in eukaryotic genes (MIDB)
1 Bioinformatics Centre, National University
of Singapore, Singapore
2 Laboratory of Computational Biology,
Ludwig Institute for Cancer Research, Sao Paulo Branch, Brazil
Received on December 5, 2000
; revised on February 14, 2001
; accepted on March 16, 2001
Motivation: Intron sliding is the relocation of intron–exon boundaries over short distances and is often also referred to as intron slippage or intron migration or intron drift. We have generated a database containing discordant intron positions in homologous genes (MIDB—Mismatched Intron DataBase). Discordant intron positions are those that are either closely located in homologous genes (within a window of 10 nucleotides) or an intron position that is present in one gene but not in any of its homologs. The MIDB database aims at systematically collecting information about mismatched introns in the genes from GenBank and organizing it into a form useful for understanding the genomics and dynamics of introns thereby helping understand the evolution of genes.
Results: Intron displacement or sliding is critically important for explaining the present distribution of introns among orthologous and paralogous genes. MIDB allows examining of intron movements and allows mapping of intron positions from homologous proteins onto a single sequence. The database is of potential use for molecular biologists in general and for researchers who are interested in gene evolution and eukaryotic gene structure. Partial analysis of this database allowed us to identify a few putative cases of intron sliding.
Availability: http://intron.bic.nus.edu.sg/midb/midb.html
Contact: meena{at}bic.nus.edu.sg
* To whom correspondence should be addressed.
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