title: Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies.
abstract: BACKGROUND
  In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding antibody maturation but also for promoting the potential engineering of the therapeutic antibodies. To date, several tools have been developed to perform such "trace-back" calculations. Yet, the predicting ability and processing volume of those tools vary significantly for different sets of data. Moreover, none of them give a confidence for immunoglobulin heavy diversity (IGHD) identification. Developing fast, efficient and enhanced tools is always needed with the booming of immunological data.
  
  
  RESULTS
  Here, a program named Ab-origin is presented. It is designed by batch query against germline databases based on empirical knowledge, optimized scoring scheme and appropriate parameters. Special efforts have been paid to improve the identification accuracy of the short and volatile region, IGHD. In particular, a threshold score for certain sensitivity and specificity is provided to give the confidence level of the IGHD identification.
  
  
  CONCLUSIONS
  When evaluated using different sets of both simulated data and experimental data, Ab-origin outperformed all the other five popular tools in terms of prediction accuracy. The features of batch query and confidence indication of IGHD identification would provide extra help to users. The program is freely available at http://mpsq.biosino.org/ab-origin/supplementary.html.
authors.affiliation: Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 320 YueYang Road, Shanghai 200031, PR China. xjwang03@sibs.ac.cn
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Wang
authors.forename: Di
authors.initials: D
authors.lastname: Wu
authors.forename: Siyuan
authors.initials: S
authors.lastname: Zheng
authors.forename: Jing
authors.initials: J
authors.lastname: Sun
authors.forename: Lin
authors.initials: L
authors.lastname: Tao
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Cao
mesh_terms: D000483:Alleles; D000906:Antibodies / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D015321:Gene Rearrangement; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D008957:Models, Genetic; D009711:Nucleotides / Q000737:chemistry; D012372:ROC Curve; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software
chemical_list: D000906:Antibodies; D007143:Immunoglobulin Heavy Chains; D009711:Nucleotides