** This is old site. [#l8d2c0ea]
** New site is [[here:http://iskana.github.io/web/]]. [#u0c43c3f]
** This is old site. The new site is [[here:http://iskana.github.io/web/]]. [#u0c43c3f]

** Kana Shimizu [#l679ade8]

Senior Research Scientist   of  National Institute of Advanced Industrial Science and Technology [[(AIST):http://cbrc3.aist.go.jp]]

Postal Address: 135-0064, 2-4-7 Aomi Koto-ku Tokyo Japan

*** Contact: shimizu-kana at aist.go.jp [#d8d8836b]
***[[Publication List]] ,  [[CV:http://cbrc3.cbrc.jp/~shimizu/CV.html]] [#r9e69b06]

*** Key words [#va126907]
Biological sequence analyses, Next-generation sequencing data analyses, Algorithm, Machine learning, Privacy-preserving data-mining

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**清水 佳奈 [#b333d17d]

産業技術総合研究所 主任研究員

住所: 〒135-0064, 東京都江東区青海2-4-7
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**Upcoming Events [#n40043c0]
We will organize [[ Privacy-aware computational genomics (PRIVAGEN 2015):http://aistcrypt.github.io/Privacy-Aware-Computational-Genomics/]]
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: An official satellite workshop of GIW/InCoB 2015 focusing on privacy-aware technologies that assist computational genomics, aiming to facilitate discussion among researchers in diverse fields including bioinformatics, genome ethics, machine learning, data-mining and cryptography.

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**Softwares [#h9073c4d]

*SLIDESORT [#s3e415b3]
[[&ref(sslogo.png,,20%);>http://cbrc3.cbrc.jp/~shimizu/slidesort]]

***Link [#h413666e]
[[Home site:http://cbrc3.cbrc.jp/~shimizu/slidesort/]]
***Executable binaries and C++ libraries: [#ja622f69]
[[For Windows PC, Linux PC with intel 64bit :http://cbrc3.cbrc.jp/~shimizu/slidesort/index.php?Download]]
***Reference [#v9d77969]
Shimizu K, Tsuda K, SlideSort: All pairs similarity search for short reads. Bioinformatics (2011) 27 (4): 464-470. [[(pubmed link):http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035798/]]

*ANGLE [#t11a427e]
&ref(angle.jpg,,100%);
***Download [#zddbe95d]
The following programs are used under BSD lisence. 
-[[For Linux PC 64bit:http://cbrc3.cbrc.jp/~shimizu/soft/ANGLE-UNIX-STATIC.TGZ]]
-[[For Linux PC source for training:http://www.cbrc.jp/~shimizu/soft/ANGLE-TRAINING.zip]]
-[[For Linux PC source :http://cbrc3.cbrc.jp/~shimizu/soft/ANGLE-UNIX-SRC.zip]]
-For windows PC (Comming soon) 

***Reference [#dbb89f98]
-Shimizu, K., Adachi, J., and Muraoka, Y. (2006) ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA. J Bioinform Comput Biol 4, 649-664 

*POODLE [#p629a4dd]
[[&ref(poodle.png,,100%);>http://mbs.cbrc.jp/poodle/]]

***Link [#u132646d]
[[Web server:http://mbs.cbrc.jp/poodle/]]
***Reference [#e23c8930]
-Shimizu, K., Hirose, S., and Noguchi, T. (2007) POODLE-S: Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position specific scoring matrix. Bioinformatics, 23, 2337-8
-Shimizu, K., Muraoka, Y., Hirose, S., Tomii, K., and Noguchi, T. (2007) Predicting mostly disordered proteins by using structure-unknown protein data. BMC Bioinformatics 8, 78
-Shimizu, K., Hirose, S., Inoue, N., Kanai, S., and Noguchi, T. (2006) POODLE: predicting protein disorder using machine-learning approaches. In Proceedings of CASP7 pp. 22-23 
(Our team was invited to CASP7 meeting as a discussion panelist of disorder prediction.)
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