Programs

CpG Island Finder classifies a genomic region to be CpG or non-CpG related. This program uses a sliding window of 201 bp in length and calculates the dinucleotide percentage for each window. The maximum of these CpG percentages is designated the CpG score and corresponding window as the CpG window. Sequences with score greater than 6.5 are classified as CpG related. For further details you may read Computational identification of promoters and first exons in the human genome. Davuluri RV, Grosse I and Zhang MQ. 2001. Nat. Genet. 29:412-17.

P53Scanner predicts potential P53 consensus binding sites. It implements a position weight matrix built from experimentally-characterized data and comparative genomics approaches.

Developed by Dr. Davuluri, FirstEF predicts the first exon and promoter regions in the human genome. The probabilistic models are designed to find potential first splice-donor sites as well as CpG-related and non-CpG-related promoter regions based on discriminant analysis. For every potential first splice-donor site and upstream promoter region, FirstEF decides whether the intermediate region could be a potential first exon based on a set of quadratic discriminant functions. Further details are available in: Computational identification of promoters and first exons in the human genome. Davuluri RV, Grosse I and Zhang MQ. 2001. Nat. Genet. 29:412-17.

We developed Genome Data Visualization Tool Kit as an application framework that consists of a set of data structures and core classes, using JavaTM technology. GDVTK is a sound framework for developing web-based applciations to present the gene regulatory region annotations in visual form. GDVTK has been implemented in the several databases developed by our group.