Skip to main content
Duke University Libraries
DukeSpace Scholarship by Duke Authors
  • Login
  • Ask
  • Menu
  • Login
  • Ask a Librarian
  • Search & Find
  • Using the Library
  • Research Support
  • Course Support
  • Libraries
  • About
View Item 
  •   DukeSpace
  • Duke Scholarly Works
  • Scholarly Articles
  • View Item
  •   DukeSpace
  • Duke Scholarly Works
  • Scholarly Articles
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

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

Thumbnail
View / Download
249.4 Kb
Date
2003-01-20
Authors
Cowell, Lindsay G
Davila, Marco
Yang, Kaiyong
Kepler, Thomas B
Kelsoe, Garnett
Repository Usage Stats
142
views
122
downloads
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.
Type
Journal article
Subject
Animals
Base Sequence
Conserved Sequence
DNA
Gene Rearrangement
Genome
Genome, Human
Humans
Mice
Models, Genetic
Models, Statistical
Molecular Sequence Data
Recombination, Genetic
Sequence Homology, Nucleic Acid
Permalink
https://hdl.handle.net/10161/10907
Collections
  • Scholarly Articles
More Info
Show full item record

Scholars@Duke

Cowell

Lindsay Grey Cowell

Adjunct Assistant Professor in the Department of Biostatistics and Bioinformatics
Somatic Diversification of Lymphocyte Antigen Receptor Genes * V(D)J Recombination * Somatic Hypermutation Biomedical Ontology * Ontological Representation of Cells of Hematopoietic Lineage Biomedical Text Mining Logic-based Reasoning
Kelsoe

Garnett H. Kelsoe

James B. Duke Distinguished Professor of Immunology
1. Lymphocyte development and antigen-driven diversification of immunoglobulin and T cell antigen receptor genes. 2. The germinal center reaction and mechanisms for clonal selection and self - tolerance. The origins of autoimmunity. 3. Interaction of innate- and adaptive immunity and the role of inflammation in lymphoid organogenesis. 4. The role of secondary V(D)J gene rearrangment in lymphocyte development and malignancies. 5. Mathematical modeling of immune responses,

Thomas B. Kepler

Adjunct Professor in the Department of Immunology
Computational and Systems Immunology, Theoretical and Evolutionary Medicine
Alphabetical list of authors with Scholars@Duke profiles.
Open Access

Articles written by Duke faculty are made available through the campus open access policy. For more information see: Duke Open Access Policy

Rights for Collection: Scholarly Articles


Works are deposited here by their authors, and represent their research and opinions, not that of Duke University. Some materials and descriptions may include offensive content. More info

Make Your Work Available Here

How to Deposit

Browse

All of DukeSpaceCommunities & CollectionsAuthorsTitlesTypesBy Issue DateDepartmentsAffiliations of Duke Author(s)SubjectsBy Submit DateThis CollectionAuthorsTitlesTypesBy Issue DateDepartmentsAffiliations of Duke Author(s)SubjectsBy Submit Date

My Account

LoginRegister

Statistics

View Usage Statistics
Duke University Libraries

Contact Us

411 Chapel Drive
Durham, NC 27708
(919) 660-5870
Perkins Library Service Desk

Digital Repositories at Duke

  • Report a problem with the repositories
  • About digital repositories at Duke
  • Accessibility Policy
  • Deaccession and DMCA Takedown Policy

TwitterFacebookYouTubeFlickrInstagramBlogs

Sign Up for Our Newsletter
  • Re-use & Attribution / Privacy
  • Harmful Language Statement
  • Support the Libraries
Duke University