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Open Access Research article

Minimal regulatory spaces in yeast genomes

Wei-Hua Chen1, Wu Wei1 and Martin J Lercher2*

Author Affiliations

1 European molecular biology laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany

2 Institute for Computer Science, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany

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BMC Genomics 2011, 12:320  doi:10.1186/1471-2164-12-320

Published: 16 June 2011

Additional files

Additional file 1:

Size distribution of old and young inter-CDS regions for the remaining eight species; this figure is complementary to Figure 1.

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Open Data

Additional file 2:

Statistics of the underrepresentation of divergent and uni-directional old pairs in the 11 yeast species. The NULL expectation here is that if all pairs are distributed randomly, at given inter-CDS range, we would expect 25% of the total pairs to be divergent, 25% to be convergent, and 50% to be co-oriented (uni-directional).

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Open Data

Additional file 3:

Reconstruction of phylogenetic relationships of the 11 analysed yeast species, using Schizosaccharomyces pombe as an outgroup. The red star indicates the location of the recent whole genome duplication (WGD). Full species names for the abbreviations are: kla - Kluyveromyces lactis, ago -Ashbya gossypii, skl - Saccharomyces kluyveri, kwa - Kluyveromyces waltii, kth - Kluyveromyces thermotolerans, zro - Zygosaccharomyces rouxii, kpo - Kluyveromyces polysporus, cgl - Candida glabrata, sca - Saccharomyces castellii, sce - Saccharomyces cerevisiae, sba - Saccharomyces bayanus, spo - Schizosaccharomyces pombe.

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Open Data

Additional file 4:

Fitting one and two Gaussians to the distributions of inter-CDS distances (log10-transformed) of old, divergently transcribed regions in the 11 analyzed yeast species.

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Additional file 5:

Modelling-B of size distribution of inter-CDS regions for the remaining eight species; this figure is complementary to Figure 3.

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Additional file 6:

Same as Figure 3& Additional file 5combined, but showing only results from simulations with 'uncorrected' distances.

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