Abstract
The chromosome 6 database (6ace) is one of a suite of databases available at the Sanger Centre, which serve the human genome sequencing communities of several chromosomes (1, 6, 20, 22, and X). Data may be retrieved in graphical or textural form using interactive windows and menus or simple command texts. The database and its management system are based on ACEDB and can be accessed via three main routes, a graphics interface, a text interface, and a Web interface. Here, we describe 6ace with particular emphasis on how to access major histocompatibility complex (MHC) and human leukocyte antigen (HLA) associated data.
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References
Durbin R. and Thierry-Mieg J. (1994) The ACEDB genome database, in Computational Methods in Genome Research (Suhai S., ed.), Plenum Press, New York, pp. 45–55.
Newell W. R., Trowsdale J., and Beck S. (1996) MHCDB database of the human MHC (release 2). Immunogenetics 45, 6–8.
Theaker A. J., Maslen G. L., Scott C. E., et al. (1997) The chromosome 6 database at the Sanger Centre. DNA Seq. 8, 167–172.
Brusic V., Rudy G., Kyne A. P., and Harrison L. C. (1998) MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res. 26, 368–371.
Avis T., Clark E. K., Flack T. L., et al. (1997) The chromosome 6 sequencing project at the Sanger Centre. DNA Seq. 8, 131–136.
Mungall A. J., Humphray S. J., Randby S. A., et al. (1997) From long range mapping to sequence-ready contigs on human chromosome 6. DNA Seq. 8, 113–154.
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.
Smit A. F. A. and Green P., unpublished results.
Sonnhammer E. L. L., and Durbin R. (1994) A workbench for large scale sequence homology analysis. Comput. Appl. Biosci. 10, 301–307.
Arnett K. L., and Parham P. (1995) HLA Class I nucleotide sequences. Tissue Antigens 46, 217–257.
Marsh S. G. E. and Bodmer J. G. (1995) HLA Class II region nucleotide sequences. Tissue Antigens 46, 258–280.
Horton R., Niblett D., Milne S., et al. (1998) Large-scale sequence comparisons reveal unusually high levels of variation in the HLADQB1 locus in the class II region of the human MHC. J. Mol. Biol. 282, 71–97.
Sayle R. A. and Milnerwhite E. J. (1995) Rasmol-biomolecular graphics for all. Trends Biochem. Sci. 20, 374–376.
Islam, S. and Sternberg, M. J. E., unpublished results (http://www/ sbg.ic.ac.uk/prepi/).
Shannon C. E. and Weaver W. (1949) The Mathematical Theory of Communication. University of Illinois Press, Urbana.
Parker K. C., Bednarek M. A., and Coligan J. E. (1994) Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J. Immunol. 152, 163–175.
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Horton, R., Beck, S. (2003). Accessing HLA Sequencing Data Through the 6ace Database. In: Powis, S.H., Vaughan, R.W. (eds) MHC Protocols. Methods in Molecular Biology™, vol 210. Humana Press. https://doi.org/10.1385/1-59259-291-0:23
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DOI: https://doi.org/10.1385/1-59259-291-0:23
Publisher Name: Humana Press
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