IgTree: creating Immunoglobulin variable region gene lineage trees

Journal of Immunological Methods
Michal BarakRamit Mehr

Abstract

Lineage trees describe the microevolution of cells within an organism. They have been useful in the study of B cell affinity maturation, which is based on somatic hypermutation of immunoglobulin genes in germinal centers and selection of the resulting mutants. Our aim was to create and implement an algorithm that can generate lineage trees from immunoglobulin variable region gene sequences. The IgTree program implements the algorithm we developed, and generates lineage trees. Original sequences found in experiments are assigned to either leaves or internal nodes of the tree. Each tree node represents a single mutation separating the sequences. The mutations that separate the sequences from each other can be point mutations, deletions or insertions. The program can deal with gaps and find potential reversion mutations. The program also enumerates mutation frequencies and sequence motifs around each mutation, on a per-tree basis. The algorithm has proven useful in several studies of immunoglobulin variable region gene mutations.

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Citations

Sep 11, 2009·Nucleic Acids Research·Michal BarakRamit Mehr
Nov 20, 2012·The Journal of Clinical Investigation·H-Christian von BüdingenStephen L Hauser
Aug 28, 2013·Journal of Clinical Bioinformatics·Miri MichaeliRamit Mehr
Jan 23, 2014·Nature Immunology·Brian A KiddJoel T Dudley
Mar 13, 2014·Bioinformatics·Jason A Vander HeidenSteven H Kleinstein
Jul 26, 2014·Brain : a Journal of Neurology·Eduardo BeltránKlaus Dornmair
Aug 8, 2014·Science Translational Medicine·Arumugam PalanichamyH-Christian von Büdingen
Oct 13, 2014·Trends in Immunology·Jorg J A Calis, Brad R Rosenberg
Nov 29, 2015·European Journal of Immunology·Hilla Tabibian-KeissarIris Barshack
Sep 2, 2015·Proceedings of the National Academy of Sciences of the United States of America·Bettina BudeusRalf Küppers
Jun 10, 2015·Clinical Immunology : the Official Journal of the Clinical Immunology Society·Jorunn N JohansenTrygve Holmøy
Jan 1, 2014·Annals of Neurology·Jaishree BankotiH-Christian von Büdingen
Jan 28, 2010·European Journal of Immunology·Neta S ZuckermanRamit Mehr
Dec 18, 2013·European Journal of Immunology·Donna McIntyreDavid I Stott
Jun 13, 2015·Bioinformatics·Namita T GuptaSteven H Kleinstein
Nov 4, 2015·Journal of Immunology Research·William D Lees, Adrian J Shepherd
Jul 22, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Connor O McCoyFrederick A Matsen
Jul 22, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Uri Hershberg, Eline T Luning Prak
Apr 14, 2015·Trends in Immunology·Keaton StagamanKaren Guillemin
Dec 24, 2014·Molecular Biology and Evolution·Alexander MirskyMaria Anisimova
Oct 29, 2015·Trends in Immunology·Victor GreiffSai T Reddy
Feb 24, 2018·Molecular Biology and Evolution·William S DeWittFrederick A Matsen
Feb 2, 2017·Frontiers in Immunology·Donald W LeeSidhartha Chaudhury
Feb 8, 2020·Neurology. Neuroimmunology and Neuroinflammation·Klaus Lehmann-HornH-Christian von Büdingen
Jul 11, 2020·PLoS Computational Biology·Mathilde FoglieriniLaurent Perez
Jan 1, 2014·The Journal of Immunology : Official Journal of the American Association of Immunologists·Mohamed UdumanSteven H Kleinstein
Aug 18, 2020·International Immunology·Huifang LiMate Tolnay
Jun 8, 2017·Annals of Clinical and Translational Neurology·Markus C KowarikJeffrey L Bennett

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