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This article is part of the supplement: The ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS)

Open Access Research

Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif

Shunfu Xu13*, Chao Zhang23, Yi Miao4, Jianjiong Gao23 and Dong Xu23*

Author Affiliations

1 Department of Gastroenterology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu 210029, China

2 Department of Computer Science, University of Missouri, Columbia, MO 65211, USA

3 C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA

4 Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Jiangsu 210029, China

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BMC Genomics 2010, 11(Suppl 3):S1  doi:10.1186/1471-2164-11-S3-S1

Published: 1 December 2010

Additional files

Additional File 1:

Top 10 genuses and species containing most proteins with at least two copies of EPIYA motif for each group.

Format: DOC Size: 18KB Download file

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Open Data

Additional File 2:

List of proteins that contain at least 4 EPIYA motifs. Parenthesis under Lotus: number of sequences; “*”: effector confirmed by experiment; “Repeats”: occurrence of EPIYA motif in a protein sequence.

Format: DOC Size: 132KB Download file

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Open Data

Additional File 3:

EPIYA motif, together with the corresponding functions of those effectors. *: predicted effectors; **: predicted motifs.

Format: DOC Size: 297KB Download file

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Open Data

Additional File 4:

This file contains a list of sequences that are similar to the KK motif in bacteria and protista.

Format: DOC Size: 151KB Download file

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Additional File 5:

This file contains a list of sequences that are similar to the R4 motif in bacteria and protista.

Format: DOC Size: 241KB Download file

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Open Data

Additional File 6:

This file contains a list of sequences that are similar to the Tarp motif in bacteria and protista.

Format: DOC Size: 84KB Download file

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Additional File 7:

This file contains a list of sequences that are similar to the Tir motif in bacteria and protista.

Format: DOC Size: 136KB Download file

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Open Data

Additional File 8:

This file contains top three subcellular localization prediction results of each predicted effector using gram-negative bacterium or eukaryote as the hosting organism, respectively. The values indicate the confidence of the predictions and “*” represents most likely localization.

Format: DOC Size: 14KB Download file

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Open Data