iHMMune-align statistics

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

Information


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

Maintainer


  • person_outline Bruno Gaeta <>

Information


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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Maintainer


  • person_outline Bruno Gaeta <>

Publication for iHMMune-align

iHMMune-align in publications

 (5)
PMCID: 5005336
PMID: 27630639
DOI: 10.3389/fimmu.2016.00336

[…] 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 ), […]

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

[…] summarize the extent to which assignments cluster together clonally derived sequences., 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 […]

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

[…] the isotype of each sequence. where duplicate sequences were identified, if they varied in length, only the longest sequence was retained for analysis. sequences were then partitioned with the ihmmune-align program , against a germline gene repertoire containing all unique ighv, ighd and ighj genes in the unswig repertoire (http://www.ihmmune.unsw.edu.au/unswig.php) and the imgt […]

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

[…] below a defined threshold. several programs are already used by the scientific community to study the b cell mutational patterns, such as soda (volpe et al., ), soda2 (munshaw and kepler, ), and ihmmune-align (gaëta et al., ) which perform v(d)j segment identification; identification of clonally-related ig gene sequences using clustering methods (chen et al., ); clustalw2 (larkin et al., ), […]

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

[…] for identifying sets of clonally-related sequences in large human immunoglobulin heavy chain gene variable region sequence sets. the program processes sequences that have been partitioned using ihmmune-align, and uses pairwise comparisons of cdr3 sequences and similarity in ighv and ighj germline gene assignments to construct a distance matrix. agglomerative hierarchical clustering […]


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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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