Document Detail


SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements.
MedLine Citation:
PMID:  20147303     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MOTIVATION: The inference of pre-mutation immunoglobulin (Ig) rearrangements is essential in the study of the antibody repertoires produced in response to infection, in B-cell neoplasms and in autoimmune disease. Often, there are several rearrangements that are nearly equivalent as candidates for a given Ig gene, but have different consequences in an analysis. Our aim in this article is to develop a probabilistic model of the rearrangement process and a Bayesian method for estimating posterior probabilities for the comparison of multiple plausible rearrangements. RESULTS: We have developed SoDA2, which is based on a Hidden Markov Model and used to compute the posterior probabilities of candidate rearrangements and to find those with the highest values among them. We validated the software on a set of simulated data, a set of clonally related sequences, and a group of randomly selected Ig heavy chains from Genbank. In most tests, SoDA2 performed better than other available software for the task. Furthermore, the output format has been redesigned, in part, to facilitate comparison of multiple solutions. AVAILABILITY: SoDA2 is available online at https://hippocrates.duhs.duke.edu/soda. Simulated sequences are available upon request.
Authors:
Supriya Munshaw; Thomas B Kepler
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2010-02-09
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  26     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2010 Apr 
Date Detail:
Created Date:  2010-03-26     Completed Date:  2010-06-21     Revised Date:  2010-09-28    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  867-72     Citation Subset:  IM    
Affiliation:
Center for Computational Immunology, Computational Biology and Bioinformatics Program, Duke University, Durham, NC 27705, USA.
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
B-Lymphocytes / immunology
Base Sequence
Gene Rearrangement, B-Lymphocyte*
Genes, Immunoglobulin*
Immunoglobulins / genetics*
Markov Chains*
Molecular Sequence Data
Sequence Alignment
Software*
Chemical
Reg. No./Substance:
0/Immunoglobulins
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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