Ab-origin: An improved tool of heavy chain rearrangement analysis for human immunoglobulin

Xiaojing Wang, Wu Wei, Siyuan Zheng, Z. W. Cao, Yixue Li

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

An improved tool to explore the origin of human immunoglobulin heavy chains, named Ab-origin, has been developed. It can analyze in detail the V-D-J joints from the rearranged sequence by searching against germline databases. In addition to the known information about antibody recombination, appropriate score system and restriction of searching location are also incorporated to improve computing performance. When compared with a newly developed software SoDA, Ab-origin performed much better in both accuracy and stability, with 2, 7 and 1 percent higher for V, D and J respectively. Though only taking the human heavy chain for an example here, the algorithm also suits for the analysis of all immunoglobulin and TCR sequences.

Original languageEnglish (US)
Title of host publicationComputational Science - ICCS 2007 - 7th International Conference, Proceedings
Pages363-369
Number of pages7
EditionPART 2
StatePublished - Dec 1 2007
Externally publishedYes
Event7th International Conference on Computational Science, ICCS 2007 - Beijing, China
Duration: May 27 2007May 30 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
NumberPART 2
Volume4488 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other7th International Conference on Computational Science, ICCS 2007
CountryChina
CityBeijing
Period5/27/075/30/07

Fingerprint

Immunoglobulin
Rearrangement
Antibodies
Antibody
Recombination
Percent
Restriction
Software
Computing
Human

Keywords

  • Antibody diversity
  • V(D)J recombination

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Wang, X., Wei, W., Zheng, S., Cao, Z. W., & Li, Y. (2007). Ab-origin: An improved tool of heavy chain rearrangement analysis for human immunoglobulin. In Computational Science - ICCS 2007 - 7th International Conference, Proceedings (PART 2 ed., pp. 363-369). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4488 LNCS, No. PART 2).

Ab-origin : An improved tool of heavy chain rearrangement analysis for human immunoglobulin. / Wang, Xiaojing; Wei, Wu; Zheng, Siyuan; Cao, Z. W.; Li, Yixue.

Computational Science - ICCS 2007 - 7th International Conference, Proceedings. PART 2. ed. 2007. p. 363-369 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4488 LNCS, No. PART 2).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Wang, X, Wei, W, Zheng, S, Cao, ZW & Li, Y 2007, Ab-origin: An improved tool of heavy chain rearrangement analysis for human immunoglobulin. in Computational Science - ICCS 2007 - 7th International Conference, Proceedings. PART 2 edn, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), no. PART 2, vol. 4488 LNCS, pp. 363-369, 7th International Conference on Computational Science, ICCS 2007, Beijing, China, 5/27/07.
Wang X, Wei W, Zheng S, Cao ZW, Li Y. Ab-origin: An improved tool of heavy chain rearrangement analysis for human immunoglobulin. In Computational Science - ICCS 2007 - 7th International Conference, Proceedings. PART 2 ed. 2007. p. 363-369. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2).
Wang, Xiaojing ; Wei, Wu ; Zheng, Siyuan ; Cao, Z. W. ; Li, Yixue. / Ab-origin : An improved tool of heavy chain rearrangement analysis for human immunoglobulin. Computational Science - ICCS 2007 - 7th International Conference, Proceedings. PART 2. ed. 2007. pp. 363-369 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2).
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