This article is part of the supplement: Seventh International Conference on Bioinformatics (InCoB2008)
Research
Flanking signal and mature peptide residues influence signal peptide cleavage
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* Corresponding author: Shoba Ranganathan shoba.ranganathan@mq.edu.au
1 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
2 Department of Chemistry and Biomolecular Sciences & ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
BMC Bioinformatics 2008, 9(Suppl 12):S15 doi:10.1186/1471-2105-9-S12-S15
Published: 12 December 2008Additional files
Additional file 1:
Curated dataset used to perform this analysis. 2352 secretory sequences containing amino-terminal SPs extracted and filtered from SPdb deposited into three worksheets, arranged according to the three organism groups namely eukaryotes, Gram-positive and Gram-negative bacteria. Each worksheet contains 7 columns of data namely Entry_name, Description (of the protein), Organism, SP_Length (length of the signal peptide), Prot_length (length of the protein sequence), Signal Peptide (signal peptide sequence), Mature Peptide (mature peptide starting from P1' and stops at the first 30 residues).
Format: XLS Size: 695KB Download file
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Additional file 2:
Frequency matrix for eukaryotes and bacteria datasets. Amino acid frequency matrix for the signal peptides and mature peptides of eukaryotes and bacteria. Percentage occupancy values from P10 to P10' [-10, +10] are shown, with the cleavage site in dotted line at -1/+1. Significant high and low values, in bold font are highlighted:grey: >10%; black: most preferred residue(s); cyan: charged residue group and green: aliphatic group.
Format: PDF Size: 80KB Download file
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