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chevron_left V(D)J assignment Immunoglobulin rearrangement detection chevron_right
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iHMMune-align specifications


Unique identifier OMICS_20615
Name iHMMune-align
Interface Web user interface
Restrictions to use None
Input data Some sequences.
Input format FASTA
Output format CSV, HTML
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Bruno Gaeta


Unique identifier OMICS_20615
Name iHMMune-align
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes




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  • person_outline Bruno Gaeta

Publication for iHMMune-align

iHMMune-align citations


High Throughput Sequencing Based Immune Repertoire Study during Infectious Disease

Front Immunol
PMCID: 5005336
PMID: 27630639
DOI: 10.3389/fimmu.2016.00336

[…] g the ImMunoGeneTics database (http://www.imgt.org) (), despite the controversies about its validity (–). New V–D–J gene annotation tools based on various algorithms are reported, such as IgBLAST (), iHMMune-align (), and Decombinator (, ) (Table ). In addition, many integrated bioinformatic tools (MiTCR, LymAnalyzer, Change-O, etc.) for data processing are developed recently (–) (Table ), which p […]


Assigning and visualizing germline genes in antibody repertoires

PMCID: 4528417
PMID: 26194754
DOI: 10.1098/rstb.2014.0240

[…] We compared IgSCUEAL with several other tools, including IMGT/HighV-QUEST v. 1.3.1 [], IgBLAST v. 1.4.0 [] and iHMMune-Align (1-06-2007) []. A binary version of SoDA (Somatic Diversification Analysis, v. 1.1) was extracted from Automation [], and Python scripts were used to run SoDA for each query sequence and […]


IgE Associated IGHV Genes from Venom and Peanut Allergic Individuals Lack Mutational Evidence of Antigen Selection

PLoS One
PMCID: 3934916
PMID: 24586993
DOI: 10.1371/journal.pone.0089730

[…] of IgE sequences in each dataset that came from venom sensitive and peanut sensitive individuals are shown in .Analysis of IGHV, IGHD and IGHJ genes in the VDJ rearrangements was performed using the iHMMune-align program. VDJ rearrangements were seen that utilized a very wide range of IGHV, IGHD and IGHJ germline genes. All IGHD and IGHJ genes were seen amongst the IgE and IgG sequences of each d […]


The Shape of the Lymphocyte Receptor Repertoire: Lessons from the B Cell Receptor

Front Immunol
PMCID: 3759170
PMID: 24032032
DOI: 10.3389/fimmu.2013.00263

[…] es within VDJ rearrangements a challenging but achievable research goal. Pursuit of this goal has driven the development of immunoglobulin gene alignment utilities including SODA2 (), IgBLAST (), and iHMMune-align (). The objective measurement of the performance of these utilities is made difficult, however, by a lack of appropriate data sets. Ideally, performance would be measured using rearrange […]


Automated cleaning and pre processing of immunoglobulin gene sequences from high throughput sequencing

Front Immunol
PMCID: 3531709
PMID: 23293637
DOI: 10.3389/fimmu.2012.00386

[…] y the GL V(D)J segments used in the unmutated (ancestor) sequences, and then assign the sequences into clonally-related groups. For gene segment identification, we use either SoDA (Volpe et al., ) or iHMMune-align (Gaëta et al., ). Our automated pipeline, which follows the above-described processes of cleaning the data, removing indels and identifying GL segments, contains our program “Ig_Clone_Fi […]


Clustering based identification of clonally related immunoglobulin gene sequence sets

Immunome Res
PMCID: 2946782
PMID: 20875155
DOI: 10.1186/1745-7580-6-S1-S4

[…] une diseases [,].Previous studies have demonstrated the importance and potential of accurate alignment and analysis for studying the immune response, using software such as IMGT/V-QUEST [] , SoDA [], iHMMune-align [], Ab-origin [], etc. However, none of these programs allow the direct identification of clonally-related immunoglobulin gene sets.The third complementarity determining region (CDR3) is […]

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iHMMune-align institution(s)
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia; School of Computer Science and Engineering, The University of New South Wales, Sydney, NSW, Australia; Molecular Immunogenetics Program, The Oklahoma Medical Research Foundation, Oklahoma City, OK, USA

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