An annotated catalog of inverted repeats of Caenorhabditis elegans chromosomes III and X, with observations concerning odd/even biases and conserved motifs.
We have taken a computational approach to the problem of discovering and deciphering the grammar and syntax of gene regulation in eukaryotes. A logical first step is to produce an annotated catalog of all regulatory sites in a given genome. Likely candidates for such sites are direct and indirect repeats, including three subcategories of indirect repeats: inverted (palindromic), everted, and mirror-image repeats. To that end we have produced a searchable database of inverted repeats of chromosomes III and X of Caenorhabditis elegans, the first completely sequenced multicellular eukaryote. Initial results from the use of this catalog are observations concerning odd/even biases in perfect IRs. The potential usefulness of the catalog as a discovery tool for promoters was shown for some of the genes involved with G-protein functions and for heat shock protein 104 (hsp104).
LeBlanc
M D
MD
Department of Math and Computer Science, Wheaton College, Norton, Massachusetts 02766, USA.
Aspeslagh
G
G
Buggia
N P
NP
Dyer
B D
BD
D000465:Algorithms; D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics*; D016208:Databases, Factual; D017238:Genes, Helminth / Q000235:genetics*; D006360:Heat-Shock Proteins / Q000235:genetics; D015801:Helminth Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D012091:Repetitive Sequences, Nucleic Acid; D029701:Saccharomyces cerevisiae Proteins
D006360:Heat-Shock Proteins; D015801:Helminth Proteins; D029701:Saccharomyces cerevisiae Proteins; C070972:HsP104 protein, S cerevisiae