title: iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia. bgaeta@cse.unsw.edu.au
authors.forename: Bruno A
authors.initials: BA
authors.lastname: Gaëta
authors.forename: Harald R
authors.initials: HR
authors.lastname: Malming
authors.forename: Katherine J L
authors.initials: KJ
authors.lastname: Jackson
authors.forename: Michael E
authors.initials: ME
authors.lastname: Bain
authors.forename: Patrick
authors.initials: P
authors.lastname: Wilson
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Collins
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D015321:Gene Rearrangement / Q000235:genetics*; D005803:Genes, Immunoglobulin; D018095:Germ-Line Mutation / Q000235:genetics* / Q000276:immunology*; D007136:Immunoglobulins / Q000235:genetics*; D008390:Markov Chains; D008957:Models, Genetic; D018448:Models, Immunological; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
chemical_list: D007136:Immunoglobulins