MOTIVATION: Immunoglobulin heavy chain (IGH) genes in mature B lymphocytes are the result of recombination of IGHV, IGHD and IGHJ germline genes, followed by somatic mutation. The correct identification of the germline genes that make up a variable VH domain is essential to our understanding of the process of antibody diversity generation as well as to clinical investigations of some leukaemias and lymphomas. RESULTS: We have developed iHMMune-align, an alignment program that uses a hidden Markov model (HMM) to model the processes involved in human IGH gene rearrangement and maturation. The performance of iHMMune-align was compared to that of other immunoglobulin gene alignment utilities using both clonally related and randomly selected IGH sequences. This evaluation suggests that iHMMune-align provides a more accurate identification of component germline genes than other currently available IGH gene characterization programs. AVAILABILITY: iHMMune-align cross-platform Java executable and web interface are freely available to academic users and can be accessed at http://www.emi.unsw.edu.au/~ihmmune/.
MOTIVATION: Immunoglobulin heavy chain (IGH) genes in mature B lymphocytes are the result of recombination of IGHV, IGHD and IGHJ germline genes, followed by somatic mutation. The correct identification of the germline genes that make up a variable VH domain is essential to our understanding of the process of antibody diversity generation as well as to clinical investigations of some leukaemias and lymphomas. RESULTS: We have developed iHMMune-align, an alignment program that uses a hidden Markov model (HMM) to model the processes involved in humanIGH gene rearrangement and maturation. The performance of iHMMune-align was compared to that of other immunoglobulin gene alignment utilities using both clonally related and randomly selected IGH sequences. This evaluation suggests that iHMMune-align provides a more accurate identification of component germline genes than other currently available IGH gene characterization programs. AVAILABILITY: iHMMune-align cross-platform Java executable and web interface are freely available to academic users and can be accessed at http://www.emi.unsw.edu.au/~ihmmune/.
Authors: Jiang Zhu; Xueling Wu; Baoshan Zhang; Krisha McKee; Sijy O'Dell; Cinque Soto; Tongqing Zhou; Joseph P Casazza; James C Mullikin; Peter D Kwong; John R Mascola; Lawrence Shapiro Journal: Proc Natl Acad Sci U S A Date: 2013-10-08 Impact factor: 11.205
Authors: Namita T Gupta; Jason A Vander Heiden; Mohamed Uduman; Daniel Gadala-Maria; Gur Yaari; Steven H Kleinstein Journal: Bioinformatics Date: 2015-06-10 Impact factor: 6.937
Authors: Katherine J L Jackson; Yi Liu; Krishna M Roskin; Jacob Glanville; Ramona A Hoh; Katie Seo; Eleanor L Marshall; Thaddeus C Gurley; M Anthony Moody; Barton F Haynes; Emmanuel B Walter; Hua-Xin Liao; Randy A Albrecht; Adolfo García-Sastre; Javier Chaparro-Riggers; Arvind Rajpal; Jaume Pons; Birgitte B Simen; Bozena Hanczaruk; Cornelia L Dekker; Jonathan Laserson; Daphne Koller; Mark M Davis; Andrew Z Fire; Scott D Boyd Journal: Cell Host Microbe Date: 2014-06-26 Impact factor: 21.023
Authors: Jason A Vander Heiden; Gur Yaari; Mohamed Uduman; Joel N H Stern; Kevin C O'Connor; David A Hafler; Francois Vigneault; Steven H Kleinstein Journal: Bioinformatics Date: 2014-03-10 Impact factor: 6.937