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. 2013 Jul;41(Web Server issue):W34-40.
doi: 10.1093/nar/gkt382. Epub 2013 May 13.

IgBLAST: an immunoglobulin variable domain sequence analysis tool

Jian Ye  1 , Ning Ma, Thomas L Madden, James M Ostell
Affiliations

IgBLAST: an immunoglobulin variable domain sequence analysis tool

Jian Ye et al. Nucleic Acids Res. 2013 Jul.

Abstract

The variable domain of an immunoglobulin (IG) sequence is encoded by multiple genes, including the variable (V) gene, the diversity (D) gene and the joining (J) gene. Analysis of IG sequences typically requires identification of each gene, as well as a comparison of sequence variations in the context of defined regions. General purpose tools, such as the BLAST program, have only limited use for such tasks, as the rearranged nature of an IG sequence and the variable length of each gene requires multiple rounds of BLAST searches for a single IG sequence. Additionally, manual assembly of different genes is difficult and error-prone. To address these issues and to facilitate other common tasks in analysing IG sequences, we have developed the sequence analysis tool IgBLAST (http://www.ncbi.nlm.nih.gov/igblast/). With this tool, users can view the matches to the germline V, D and J genes, details at rearrangement junctions, the delineation of IG V domain framework regions and complementarity determining regions. IgBLAST has the capability to analyse nucleotide and protein sequences and can process sequences in batches. Furthermore, IgBLAST allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene.

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Figures

Figure 1.
Figure 1.
IgBLAST result page. This example used a human IG sequence (GenBank accession AY671579) to search against the default germline gene databases [IMGT human V genes (F + ORF + in-frame P), IMGT human D genes (F + ORF) and IMGT human J genes (F + ORF)]. The search used default values for all parameters. A red box was added to indicate the overlapping nucleotides TAC at the D–J junction. The search was performed on 25 February 2013.
Figure 2.
Figure 2.
Example IgBLAST result of searching against the germline gene databases and the NCBI nr database simultaneously. A mouse IG sequence (GenBank accession AF104468) was searched against the default mouse germline gene databases [IMGT mouse V genes (F + ORF + in-frame P), IMGT mouse D genes (F + ORF + in-frame P) and IMGT mouse J genes (F + ORF + in-frame P)]. The ‘organism’ field was set to mouse, and the nr database was selected for the ‘additional database’ field. Default values are used for all other parameters, except the ‘number of alignments for additional database’ was 25. The light blue pop-up message box is a feature that displays the sequence title when the mouse pointer is moved over the sequence identifier (i.e. the accession AF021857 in the example). Only part of the result page is shown because of space limitation. A red box was added to indicate the hits from the nr databases that have 100% matches to the query over the 290 bases. The search was performed on 25 February 2013.
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References

    1. Lefranc M-P, Lefranc G. The Immunoglobulin Factsbook. San Diego: Academic Press; 2001.
    1. Schatz DG, Oettinger MA, Schlissel MS. V(D)J recombination: molecular biology and regulation. Annu. Rev. Immunol. 1992;10:359–383. - PubMed
    1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
    1. Yousfi Monod M, Giudicelli V, Chaume D, Lefranc MP. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics. 2004;20(Suppl. 1):i379–i385. - PubMed
    1. Brochet X, Lefranc MP, Giudicelli V. IMGT/V-QUEST: the highly customized and integrated system for Ig and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res. 2008;36:W503–W508. - PMC - PubMed

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