Abstract
Scientists working in the human leukocyte antigen (HLA) field have access to a number of different informatics resources for the analysis and interpretation of HLA sequences. Recent advances in bioinformatics have resulted in an increase in the number of tools and facilities available for sequence analysis. Researchers can now utilize these tools to analyze the genomic information within their own field; in addition, the HLA field also has a number of groups developing software specifically for this area. Within this chapter, we will be discussing both the more general tools and the specialist HLA informatics tools available.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Baker W., van den Broek A., Camon E., Hingamp P., Sterk P., Stoesser G., and Tuli M. A. (2000) The EMBL nucleotide sequence database. Nucleic Acids Res. 28, 19–23.
Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J., Rapp B. A., and Wheeler D. L. (2000) GenBank. Nucleic Acids Res. 28, 15–18.
Tateno Y., Miyazaki S., Ota M., Sugawara H., and Gojobori T. (2000) DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res. 28, 24–26.
Bairoch A. and Apweiler R. (2000) The SWISS-PROT protein se-quence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48.
Altschul S. F., Gish W., Miller W., Myers E. W., and Lipman D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
Altschul S. F., Madden T. L., Schaffer A. A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.
Etzold T., Ulyanov A., and Argos P. (1996) SRS: information re-trieval system for molecular biology data banks. Methods Enzymol. 266, 114–128.
Schuler G. D., Epstein J. A., Ohkawa H., and Kans J. A. (1996) Entrez: molecular biology database and retrieval system. Methods Enzymol. 266, 141–162.
Harger C., Chen G., Farmer A., et al. (2000) The Genome Sequence DataBase. Nucleic Acids Res. 28, 31–32.
Talbot C. C. and Cutticchia A. J. (1999) Human Mapping Databases, Current Protocols in Human Genetics. John Wiley & Sons New York, pp. 1.13.1–1.13.12.
Bodmer J. G., Marsh S. G., Albert E. D., et al. (1999) Nomenclature for factors of the HLA system, 1998. Tissue Antigens 53, 407–446.
Newell W. R., Trowsdale J., and Beck S. (1994) MHCDB—data-base of the human MHC. Immunogenetics 40, 109–115.
Newell W. R., Trowsdale J., and Beck S. (1996) MHCDB: data-base of the human MHC (release 2). Immunogenetics 45, 6–8.
Brusic V., Rudy G. and Harrison L. C. (1998) MHCPEP, a data-base of MHC-binding peptides: update 1997. Nucleic Acids Res. 26, 368–371.
Lehvaslaiho H., Stupka E. and Ashburner M. (2000) Sequence variation database project at the European Bioinformatics Institute. Hum. Mutat. 15, 52–56.
Robinson J., Malik A., Parham P., Bodmer J. G. and Marsh S. G. (2000) IMGT/HLA database—a sequence database for the human major histocompatibility complex. Tissue Antigens 55, 280–287.
Giudicelli V., Chaume D., Bodmer J., et al. (1997) IMGT, the inter-national ImMunoGeneTics database. Nucleic Acids Res. 25, 206–211.
Ruiz M., Giudicelli V., Ginestoux C., et al. (2000) IMGT, the inter-national ImMunoGeneTics database. Nucleic Acids Res. 28, 219–221.
Marsh S. G. E. (2000) Nomenclature for factors of the HLA System, update March 2000. Tissue Antigens 27, 163.
Marsh S. G. E. (2000) Nomenclature for factors of the HLA System, update March 2000. Hum. Immunol. 61, 718.
Marsh S. G. E. (2000) Nomenclature for factors of the HLA System, update March 2000. Eur. J. Immunogen. 27, 163.
Mason P. M. and Parham P. (1998) HLA class I region sequences, 1998. Tissue Antigens 51, 417–466.
Marsh S. G. E. (1998) HLA class II region sequences, 1998. Tissue Antigens 51, 467–507.
Marsh S. G. E. and Bodmer J. G. (1993) HLA Class II Sequence Databank. Hum. Immunol. 36, 44.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Humana Press Inc.
About this protocol
Cite this protocol
Robinson, J., Marsh, S.G.E. (2003). HLA Informatics. In: Powis, S.H., Vaughan, R.W. (eds) MHC Protocols. Methods in Molecular Biology™, vol 210. Humana Press. https://doi.org/10.1385/1-59259-291-0:03
Download citation
DOI: https://doi.org/10.1385/1-59259-291-0:03
Publisher Name: Humana Press
Print ISBN: 978-0-89603-548-5
Online ISBN: 978-1-59259-291-3
eBook Packages: Springer Protocols