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Open Access Methodology

An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches

Robert D Bremel* and E Jane Homan

Author Affiliations

ioGenetics LLC, 3591 Anderson Street, Madison, WI 53704, USA

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Immunome Research 2010, 6:7  doi:10.1186/1745-7580-6-7

Published: 2 November 2010

Additional files

Additional file 1:

Table S1: Listing of internet sites with relevant computing and resource sites.

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Additional file 2:

Table S2: Physicochemical Properties of amino acids used for computing the principal components.

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Additional file 3:

Table S3a: Peptides used for Neural Network training: MHC-I.

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Additional file 4:

Table S3b: Peptides used for Neural Network training: MHC-II.

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Additional file 5:

Table S4a: VIP MHC-I.

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Additional file 6:

Table S4b: VIP MHC-II.

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Additional file 7:

Table S5: Correlations among different prediction schemes using the IEDB dataset.

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Additional file 8:

Figures S5, S6, S7, and S8: Correspond to Figures 5, 6, 7, and 8and contain additional detail.

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Additional file 9:

Table S6: Random 15-mers from Staphylococcus aureus COL along with the output from multiple prediction schemes.

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