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Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum

Kevin Brick1*, Junichi Watanabe2 and Elisabetta Pizzi1

Author Affiliations

1 Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate - Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy

2 Department of Parasitology, Institute of Medical Science, The University of Tokyo 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan

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Genome Biology 2008, 9:R178  doi:10.1186/gb-2008-9-12-r178

Published: 18 December 2008

Additional files

Additional data file 1:

Physicochemical properties, property numbers, and data source for each.

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Open Data

Additional data file 2:

Key steps in the individual SVM training/feature selection and MAPP prediction processes.

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Open Data

Additional data file 3:

The averaged MAPP profiles in the region from -400 to +200 nucleotides around TSSs possibly highlight a transcription start area.

Format: PDF Size: 18KB Download file

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Open Data

Additional data file 4:

Explanation of the strand symmetry and shift observed in MAPP profiles.

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Open Data

Additional data file 5:

The upstream regions of genes for which TSSs have been mapped experimentally and independently of the Full-Malaria database.

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Open Data

Additional data file 6:

These two color-coded matrices represent the correlations between physicochemical properties. On top is the matrix for all properties, while below is that for the reduced set of non-redundant properties used for the predictor.

Format: PDF Size: 500KB Download file

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Open Data