Ab-origin specifications

Information


Unique identifier OMICS_20613
Name Ab-origin
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

Maintainers


This tool is not available anymore.

Publication for Ab-origin

Ab-origin citations

 (2)
library_books

Assigning and visualizing germline genes in antibody repertoires

2015
PMCID: 4528417
PMID: 26194754
DOI: 10.1098/rstb.2014.0240

[…] dible set of D germline alleles. Other approaches which may result in further improvement to D gene assignment include refinement of scoring schemes based on evaluation datasets, an approach taken by Ab-Origin [] to improve assignments based on BLAST, or pre-processing of the rearranged immunoglobulin to identify regions using models such as conditional random fields, an approach used by Malhotra […]

library_books

Clustering based identification of clonally related immunoglobulin gene sequence sets

2010
Immunome Res
PMCID: 2946782
PMID: 20875155
DOI: 10.1186/1745-7580-6-S1-S4

[…] revious 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 a highly variable […]

Ab-origin institution(s)
Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China; College of Life science and Biotechnology, Tongji University, Shanghai, China
Ab-origin funding source(s)
Supported in part by grants from Ministry of Science and Technology China (2004CB720103, 2006AA02Z317), National Natural Science Foundation of China (30500107), Shanghai Municipal Education Commission (2000236018, 2000236016) and Science and technology commission of Shanghai municipality (06PJ14072).

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