RSSsite

RSSsite identifies cryptic recombination signal sequences (cRSSs) in human and mouse genomes to support analysis of V(D)J recombination underlying B- and T-lymphocyte development.

Key Features:

• RSSdb: A database of pre-computed potential recombination signal sequences (cRSSs) from human and mouse genomes.
• DnaGrab: A scoring tool that evaluates potential RSSs within DNA sequences.
• Probability models and Bayesian networks: Predictive models that account for correlations between groups of nucleotide positions and can be implemented as Bayesian networks using reference sets of known RSSs.

Scientific Applications:

• Oncogenic translocation analysis: Identification of cRSSs implicated in oncogenic translocations associated with lymphoid malignancies.
• Aberrant V(D)J recombination mapping: Detection of cryptic RSSs outside immunoglobulin and TCR loci that may be targets of erroneous V(D)J cleavage.

Methodology:

Uses probability models that account for nucleotide-position correlations, can be represented as Bayesian networks trained on reference RSS sets, DnaGrab scores sequences, and RSSdb contains pre-computed candidate RSSs.