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This article is part of the supplement: Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Computational Biology

Open Access Proceedings

In silico prediction of the granzyme B degradome

Lawrence JK Wee1*, Esmond PS Er1, Lisa FP Ng23 and JC Tong13

Author Affiliations

1 Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis South Tower, Singapore 138632

2 Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648

3 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597

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BMC Genomics 2011, 12(Suppl 3):S11  doi:10.1186/1471-2164-12-S3-S11

Published: 30 November 2011

Additional files

Additional File 1:

Dataset of granzyme B cleavage sites This file contains the dataset of granzyme B cleavage sites. Training and test set sequences are listed on different tabs.

Format: XLSX Size: 80KB Download file

Open Data

Additional File 2:

SVM parameter optimization Training sets of different sequence window datasets were trained under 10-fold cross-validation using various combinations of C and γ values. The optimal C and γ values for each training set are used to train the final SVM classifier. Optimal values are indicated below the corresponding chart.

Format: PDF Size: 611KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data