IMSEQ-A fast and error aware approach to immunogenetic sequence analysis

Bioinformatics

Volumn 31, Issue 18, 2015, Pages 2963-2971

  Kuchenbecker, Leon ^a,b,c   Nienen, Mikalai ^a   Hecht, Jochen ^a,c   Neumann, Avidan U ^a,d   Babel, Nina ^a,e   Reinert, Knut ^b,c   Robinson, Peter N ^a,b,c  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^d BAR ILAN UNIVERSITY   (Israel)

^e RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOGENETICS; PROCEDURES; STANDARDS; T LYMPHOCYTE RECEPTOR GENE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENES, T-CELL RECEPTOR BETA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNOGENETICS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84941759089     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv309     Document Type: Article

References (23)

1. Arstila, T. P. et al. (1999) A direct estimate of the humanab T cell receptor diversity. Science, 286, 958-61.
2. Bolotin, D. A. et al. (2013) MiTCR: software for T-cell receptor sequencing data analysis. Nature Methods, 10, 813-814.
3. Brochet, X. et al. (2008) IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized VJ and VDJ sequence analysis. Nucleic Acids Res., 36(Suppl. 2), W503-W508.
4. Chao, K. M. et al. (1992) Aligning two sequences within a specified diagonal band. Comput. Appl. Biosci., 8, 481-487.
5. Dohm, J. C. et al. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
6. Dö ring, A., et al. (2008) SeqAn an efficient, generic C\+\+ library for sequence analysis. BMC Bioinformatics 9, 11.
7. Dziubianau, M. et al. (2013) TCR repertoire analysis by next generation sequencing allows complex differential diagnosis of T cell-related pathology. Am. J. Transplant., 13, 2842-2854.
8. Giudicelli, V. et al. (2005) IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res., 33(Suppl. 1), D256-D261.
9. Holtgrewe, M. (2010) Mason-A read simulator for second generation sequencing data. Technical report FU Berlin. Institut fü r Mathematik und Informatik, Freie Universitä t Berlin
10. Jackson, K. J. et al. (2014) Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements. Cell Host and Microbe, 16, 105-114.
11. Janeway, C. A. et al. (1999) Immunobiology: The Immune System in Health and Disease. Current Biology Publications, New York, NY.
12. Li, S. et al. (2013) IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat. Commun., 4, 2333.
13. Myers, G. (1999) A fast bit-vector algorithm for approximate string matching based on dynamic programming. J. ACM, 46, 395-415.
14. Rasmussen, K. R. et al. (2006) Efficient q-gram filters for finding all e-matches over a given length. J. Comput. Biol., 13, 296-308.
15. Shugay, M. et al. (2014) Towards error-free profiling of immune repertoires. Nat. Methods, 11, 653-655.
16. Sims, D. et al. (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet., 15, 121-132.
17. Thomas, N. et al. (2013) Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics, 29, 542-550.
18. Tonegawa, S. (1983) Somatic generation of antibody diversity. Nature, 302, 575-581.
19. Vollmers, C. et al. (2013) Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc. Natl. Acad. Sci., 110, 13463-13468.
20. Wu, D. et al. (2012) High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci. Trans. Med., 4, 134-63.
21. Yang, X. et al. (2015) TCRklass: a new k-string-based algorithm for human and mouse TCR repertoire characterization. J. Immunol., 194, 446-454.
22. Ye, J. et al. (2013) IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res., 41, W34-W40.
23. Zhang, J. et al. (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics, 30, 614-620.