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Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling.

dc.contributor.author Cowell, Lindsay G
dc.contributor.author Davila, Marco
dc.contributor.author Yang, Kaiyong
dc.contributor.author Kepler, Thomas B
dc.contributor.author Kelsoe, Garnett
dc.coverage.spatial United States
dc.date.accessioned 2015-11-18T16:43:12Z
dc.date.issued 2003-01-20
dc.identifier http://www.ncbi.nlm.nih.gov/pubmed/12538660
dc.identifier.issn 0022-1007
dc.identifier.uri https://hdl.handle.net/10161/10907
dc.description.abstract The recombination signals (RS) that guide V(D)J recombination are phylogenetically conserved but retain a surprising degree of sequence variability, especially in the nonamer and spacer. To characterize RS variability, we computed the position-wise information, a measure correlated with sequence conservation, for each nucleotide position in an RS alignment and demonstrate that most position-wise information is present in the RS heptamers and nonamers. We have previously demonstrated significant correlations between RS positions and here show that statistical models of the correlation structure that underlies RS variability efficiently identify physiologic and cryptic RS and accurately predict the recombination efficiencies of natural and synthetic RS. In scans of mouse and human genomes, these models identify a highly conserved family of repetitive DNA as an unexpected source of frequent, cryptic RS that rearrange both in extrachromosomal substrates and in their genomic context.
dc.language eng
dc.publisher Rockefeller University Press
dc.relation.ispartof J Exp Med
dc.subject Animals
dc.subject Base Sequence
dc.subject Conserved Sequence
dc.subject DNA
dc.subject Gene Rearrangement
dc.subject Genome
dc.subject Genome, Human
dc.subject Humans
dc.subject Mice
dc.subject Models, Genetic
dc.subject Models, Statistical
dc.subject Molecular Sequence Data
dc.subject Recombination, Genetic
dc.subject Sequence Homology, Nucleic Acid
dc.title Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling.
dc.type Journal article
duke.contributor.id Cowell, Lindsay G|0270702
duke.contributor.id Kepler, Thomas B|0296676
duke.contributor.id Kelsoe, Garnett|0205291
pubs.author-url http://www.ncbi.nlm.nih.gov/pubmed/12538660
pubs.begin-page 207
pubs.end-page 220
pubs.issue 2
pubs.organisational-group Basic Science Departments
pubs.organisational-group Biostatistics & Bioinformatics
pubs.organisational-group Duke
pubs.organisational-group Duke Cancer Institute
pubs.organisational-group Duke Human Vaccine Institute
pubs.organisational-group Immunology
pubs.organisational-group Institutes and Centers
pubs.organisational-group School of Medicine
pubs.publication-status Published
pubs.volume 197


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