iHMMune-align web-based access

A HMM-based Partitioning Utility for the Human Immunoglobulin Heavy Chain


iHMMune-align is an alignment tool designed specifically for modelling the antibody generation process and identifying the constituent germline genes of a human heavy chain mature variable region sequence, in order to generate an alignment of the rearranged immunoglobulin sequence with its germline genes.

Two versions of iHMMune-align are available.

Standard iHMMune-align is for full-length or near full-length sequences.

Short iHMMune-align is for short sequences, and was specifically developed to handle sequences produced using the BIOMED2 primers. These changes were made possible through the support of the Chronic Lymphocytic Leukemia Australian Research Consortium (CLLARC).

Please note that iHMMune-align is designede to align VDJ rearrangements, and does not currently handle unrearranged IGHV genes.

Use the links on the right to download iHMMune-align (Java executable) and access the iHMMune-align web interface.

If you use iHMMune-align in your research please cite:

Gaeta BA, Malming HR, Jackson KJ, Bain ME, Wilson P, Collins AM (2007) iHMMune-align: Hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. Bioinformatics 23:1580-1587


For queries about iHMMune-align:
Andrew Collins
Katherine Jackson