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Journal article
Detecting selection in immunoglobulin sequences
Nucleic acids research, v 39(suppl_2), pp W499-W504
01 Jul 2011
PMID: 21665923
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The ability to detect selection by analyzing mutation patterns in experimentally derived immunoglobulin (Ig) sequences is a critical part of many studies. Such techniques are useful not only for understanding the response to pathogens, but also to determine the role of antigen-driven selection in autoimmunity, B cell cancers and the diversification of pre-immune repertoires in certain species. Despite its importance, quantifying selection in experimentally derived sequences is fraught with difficulties. The necessary parameters for statistical tests (such as the expected frequency of replacement mutations in the absence of selection) are non-trivial to calculate, and results are not easily interpretable when analyzing more than a handful of sequences. We have developed a web server that implements our previously proposed Focused binomial test for detecting selection. Several features are integrated into the web site in order to facilitate analysis, including V(D)J germline segment identification with IMGT alignment, batch submission of sequences and integration of additional test statistics proposed by other groups. We also implement a Z-score-based statistic that increases the power of detecting selection while maintaining specificity, and further allows for the combined analysis of sequences from different germlines. The tool is freely available at http://clip.med.yale.edu/selection.
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Details
- Title
- Detecting selection in immunoglobulin sequences
- Creators
- Mohamed Uduman - Yale UniversityGur Yaari - Yale UniversityUri Hershberg - Yale UniversityJacob A. Stern - Yale UniversityMark J. Shlomchik - Yale UniversitySteven H. Kleinstein - Yale University
- Publication Details
- Nucleic acids research, v 39(suppl_2), pp W499-W504
- Publisher
- Oxford Univ Press
- Number of pages
- 6
- Grant note
- R03AI092379 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) R03AI092379-01 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000292325300081
- Scopus ID
- 2-s2.0-79959997640
- Other Identifier
- 991019167659304721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology