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Novel features of ARS selection in budding yeast Lachancea kluyveri

Ivan Liachko1, Emi Tanaka2, Katherine Cox4, Shau Chee Claire Chung4, Lu Yang4, Arael Seher4, Lindsay Hallas4, Eugene Cha4, Gina Kang4, Heather Pace4, Jasmine Barrow4, Maki Inada3, Bik-Kwoon Tye4* and Uri Keich2*

Author Affiliations

1 Department of Genome Sciences, University of Washington, Seattle, WA, USA

2 School of Mathematics and Statistics, University of Sydney, Sydney, Australia

3 Department of Biology, Ithaca College, Ithaca, NY, USA

4 Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA

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BMC Genomics 2011, 12:633  doi:10.1186/1471-2164-12-633

Published: 28 December 2011

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Additional file 1:

Supplementary Tables. The supplementary tables associated with this study.

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Additional file 2:

Supplementary Figures. The supplementary figures associated with this study. Figure S1. Additional LkARS truncation experiments. LkARS-E143 (A) and LkARS-C1177 (B) were truncated to narrow down functional regions. Black boxes represent functional LkARS fragments, red boxes represent non-functional fragments. The extent of the truncation in basepairs is indicated on the left of the graphics (L = truncated from the left, R = truncated from the right). The length of the original full-length fragment isolated from the screen is indicated next to the first fragment from the top. Figure S2. The reduced predictive power of the 11 bp LkACS. As in Figure 5, but highlighted with the best match of the 11 bp LkACS motif. This motif fails to properly identify the essential region of LkARS-C35. Figure S3. L. kluyveri auxiliary motifs. The 6 bp motif (GIMSAN p-value 0.036) appeared in 29 of the 84 LkARSs, the 14 bp motif (GIMSAN p-value 0.001) in 53 of the LkARSs and the 25 bp motif (GIMSAN p-value 0.0014) in all the sequences (using the OOPS model). Figure S4. Nucleotide distributions surrounding functionally relevant ACS motifs in ScARSs (A), LkARSs (B), and KlARSs (C).

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Additional file 3:

ARSs used in this study. A list of coordinates and functional information of the LkARSs used in this study.

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