• Login
    ARAN - Access to Research at NUI Galway
    View Item 
    •   ARAN Home
    • Support Services
    • Externally hosted open access publications with NUI Galway authors (2)
    • View Item
    •   ARAN Home
    • Support Services
    • Externally hosted open access publications with NUI Galway authors (2)
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of ARANCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsTypesThis CollectionBy Issue DateAuthorsTitlesSubjectsTypes

    My Account

    LoginRegister

    Statistics

    Most Popular ItemsStatistics by CountryMost Popular Authors

    Help

    How to submit and FAQs

    Lymanalyzer: a tool for comprehensive analysis of next generation sequencing data of t cell receptors and immunoglobulins

    Thumbnail
    View/Open
    Full Text
    Date
    2015-10-07
    Author
    Yu, Yaxuan
    Ceredig, Rhodri
    Seoighe, Cathal
    Metadata
    Show full item record
    Usage
    This item's downloads: 0 (view details)
    Cited 26 times in Scopus (view citations)
    
    Recommended Citation
    Yu, Yaxuan; Ceredig, Rhodri; Seoighe, Cathal (2015). Lymanalyzer: a tool for comprehensive analysis of next generation sequencing data of t cell receptors and immunoglobulins. Nucleic Acids Research 44 (4),
    Published Version
    https://academic.oup.com/nar/article-pdf/44/4/e31/16668078/gkv1016.pdf
    Abstract
    The adaptive immune system includes populations of B and T cells capable of binding foreign epitopes via antigen specific receptors, called immunoglobulin (IG) for B cells and the T cell receptor (TCR) for T cells. In order to provide protection from a wide range of pathogens, these cells display highly diverse repertoires of IGs and TCRs. This is achieved through combinatorial rearrangement of multiple gene segments in addition, for B cells, to somatic hypermutation. Deep sequencing technologies have revolutionized analysis of the diversity of these repertoires; however, accurate TCR/IG diversity profiling requires specialist bioinformatics tools. Here we present LymAnalzyer, a software package that significantly improves the completeness and accuracy of TCR/ IG profiling from deep sequence data and includes procedures to identify novel alleles of gene segments. On real and simulated data sets LymAnalyzer produces highly accurate and complete results. Although, to date we have applied it to TCR/ IG data from human and mouse, it can be applied to data from any species for which an appropriate database of reference genes is available. Implemented in Java, it includes both a command line version and a graphical user interface and is freely available at https://sourceforge.net/projects/lymanalyzer/.
    URI
    http://hdl.handle.net/10379/14500
    Collections
    • Externally hosted open access publications with NUI Galway authors (2)
    • Copyright @ NUI Galway
    • Library
    • NUI Galway