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Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins

Johan Nilsson1, Mats Grahn1 and Anthony PH Wright12*

Author Affiliations

1 School of Life Sciences, Södertörn University, SE-141 89 Huddinge, Sweden

2 Clinical Research Center, Novum Level 5, Department of Laboratory Medicine and Center for Biosciences, Karolinska Institutet, SE-141 86 Huddinge, Sweden

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Genome Biology 2011, 12:R65  doi:10.1186/gb-2011-12-7-r65

Published: 19 July 2011

Additional files

Additional file 1:

Yeast strain isolates used in the study.

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Additional file 2:

Non-synonymous SNPs in S. cerevisiae genes studied. The nature of each amino acid change for each changed amino acid in each strain is shown for each of 3,639 genes.

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Additional file 3:

Non-synonymous SNPs in S. paradoxus genes studied. The nature of each amino acid change for each changed amino acid in each strain is shown for each of 3,691 genes.

Format: RTF Size: 3.8MB Download file

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Additional file 4:

Synonymous SNPs in S. cerevisiae genes studied. The identity of each affected amino acid in each affected strain is shown for each of 3,737 genes.

Format: RTF Size: 3.7MB Download file

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Additional file 5:

Synonymous SNPs in S. paradoxus genes studied. The identity of each affected amino acid in each affected strain is shown for each of 3,756 genes.

Format: RTF Size: 7.2MB Download file

Open Data

Additional file 6:

Chromosomal location of protein-coding region SNPs in the different strains of S. cerevisiae. The direction of each gene as well as the base change in each SNP and its affect on codons and encoded amino acids is shown.

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Open Data

Additional file 7:

Chromosomal location of protein-coding region SNPs in the different strains of S. paradoxus. The direction of each gene as well as the base change in each SNP and its affect on codons and encoded amino acids is shown.

Format: ZIP Size: 4MB Download file

Open Data

Additional file 8:

FastA file containing the ORF DNA sequence of all analyzed S. cerevisiae genes. Strand, phase, chromosone and genomic start/finish coordinates are specified in the header line.

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Additional file 9:

FastA file containing the protein sequence translated from the ORFs of all analyzed S. cerevisiae genes.

Format: RTF Size: 1.6MB Download file

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Additional file 10:

Fraction of amino acid residues for each protein that are predicted by the PSIPRED method to adopt α-helical conformation, using a confidence value threshold of 8.

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Additional file 11:

Fraction of amino acid residues for each protein that are predicted by the PSIPRED method to adopt β-sheet conformation, using a confidence value threshold of 8.

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Open Data

Additional file 12:

Fraction of amino acid residues for each protein that are predicted by the VSL2 method to adopt intrinsically disordered conformation, using a confidence value threshold of 0.8.

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Open Data

Additional file 13:

Fraction of amino acid residues for each protein that are predicted by the VSL2 method to adopt intrinsically disordered conformation, using a confidence value threshold of 0.5.

Format: RTF Size: 99KB Download file

Open Data

Additional file 14:

Fixation index of each investigated protein coding gene along with the associated P-value. The FI was calculated using the MKtest program and is defined as the ratio (dN/dS)/(pN/pS).

Format: RTF Size: 142KB Download file

Open Data

Additional file 15:

Fixation index calculated for the merged aligned regions in α-helical, β-strand, or intrinsically disordered conformation from all analyzed proteins, with or without removal of genes with a fixation index deviating more than three standard deviations from the mean of the entire data set.

Format: RTF Size: 1KB Download file

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Additional file 16:

Amino acid positions of functional sites in each investigated protein as predicted by the Limacs method for known pfam domains mapped to the proteins.

Format: RTF Size: 72KB Download file

Open Data