Identification and utilization of arbitrary correlations in models of recombination signal sequences.

ABSTRACT: BACKGROUND:A significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites, such as protein-binding sites in regulatory DNA. Current approaches sometimes perform poorly when positions in the site do not independently affect protein binding. We developed a statistical technique for modeling the correlation structure in variable DNA sequence sites. The method places no restrictions on the number of correlated positions or on their spatial relationship within the site. No prior empirical evidence for the correlation structure is necessary. RESULTS:We applied our method to the recombination signal sequences (RSS) that direct assembly of B-cell and T-cell antigen-receptor genes via V(D)J recombination. The technique is based on

SUBMITTER: Cowell LG 

PROVIDER: S-EPMC151174 | biostudies-literature | 2002

REPOSITORIES: biostudies-literature