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Nucleic Acids Research, 2004, Vol. 32, Database issue D319-D322
© 2004 Oxford University Press

SCMD: Saccharomyces cerevisiae Morphological Database

Taro L. Saito1,2, Miwaka Ohtani1,2, Hiroshi Sawai2, Fumi Sano2,4, Ayaka Saka2,4, Daisuke Watanabe2,4, Masashi Yukawa2,4, Yoshikazu Ohya2,4 and Shinichi Morishita*,2,3

1 Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, 2 Institute for Bioinformatics and Research and Development, Japan Science and Technology Corporation, Science Plaza, 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666, Japan, 3 Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan and 4 Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan

*To whom correspondence should be addressed. Tel: +81 47 136 3984; Fax: +81 47 136 3977; Email: moris{at}gi.k.u-tokyo.ac.jp

To study the global regulation of cell morphology, a number of groups have recently reported genome-wide screening data for yeast mutants with abnormal morphology. Despite the relatively simple ellipsoidal shape of yeast cells, in the past, cell morphology researchers have processed information on cells manually. These time-consuming, entirely subjective tasks motivated us to develop image-processing software that automatically extracts yeast cells from micrographs and processes them to measure key morphological characteristics such as cell size, roundness, bud neck position angle, nuclear DNA localization and actin localization. To date, we have retrieved 960 609 cells from 52 988 micrographs of 2531 mutants using our software, and we have published the results in the Saccharomyces cerevisiae Morphological Database (SCMD), which facilitates the analysis of abnormal cells. Our system provides quantitative data for shapes of the daughter and mother cells, localization of the nuclear DNA and morphology of the actin patches. To search for mutants with similar morphological traits, the system outputs a list of mutants ranked by similarity of average morphological parameters. The SCMD is available at http://yeast. gi.k.u-tokyo.ac.jp/.


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