utgenome.org

UTGB Toolkit - Create Personalized Genome Browsers

Create Personalized Genome Browsers with UTGB Toolkit. UTGB (University of Tokyo Genome Browser) Toolkit is an open-source software for developing personalized genome browsers that work in web browsers. UTGB Toolkit has following features:. UTGB uses AJAX-based web interfaces to avoid excessive reloading of web pages. The UTGB Toolkit is licensed under an open source license. And is freely available for both commercial and personal use. Create a your own genome browser. UTGB Toolkit User's Manual. This w...

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Taro Saito

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JP

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Taro Saito

5-1-5 ●●●●●●wanoha

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UTGB Toolkit - Create Personalized Genome Browsers | utgenome.org Reviews

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Create Personalized Genome Browsers with UTGB Toolkit. UTGB (University of Tokyo Genome Browser) Toolkit is an open-source software for developing personalized genome browsers that work in web browsers. UTGB Toolkit has following features:. UTGB uses AJAX-based web interfaces to avoid excessive reloading of web pages. The UTGB Toolkit is licensed under an open source license. And is freely available for both commercial and personal use. Create a your own genome browser. UTGB Toolkit User's Manual. This w...

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UTGB Toolkit - Create Personalized Genome Browsers | utgenome.org Reviews

https://utgenome.org

Create Personalized Genome Browsers with UTGB Toolkit. UTGB (University of Tokyo Genome Browser) Toolkit is an open-source software for developing personalized genome browsers that work in web browsers. UTGB Toolkit has following features:. UTGB uses AJAX-based web interfaces to avoid excessive reloading of web pages. The UTGB Toolkit is licensed under an open source license. And is freely available for both commercial and personal use. Create a your own genome browser. UTGB Toolkit User's Manual. This w...

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wormtss.utgenome.org

WormTSS: The Primary Transcriptome of C.elegans

WormTSS: The Primary Transcriptome of C. elegans. Despite the fundamental importance of transcription start sites (TSSs), little is known about TSSs in C. elegans. This is due to the high frequency of. MRNAs, a process which post-transcriptionally removes RNA segments of variable length from the 5'end of mature mRNAs. WormTSS. Powerd by UTGB Toolkit.

yeast.utgenome.org

Yeast UT Genome Browser

Yeast ut genome browser. Yeast UT Genome Browser was closed. We are sorry that we have terminated the web service to browse the cDNA data described in Miura et al. (2006) due to a security concern. The data can be browsed as a track named cDNA transcripts: Miura et al. (2006) in the genome browser at Saccharomyces Genome Database (SGD). All the data can be downloaded from Life Science Database Archive maintained by National Bioscience Database Center (NBDC).

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UTGB Toolkit - Information for UTGB Developers

http://utgenome.org/development.html

Information for UTGB Developers. We migrated the source code repository from Subversion to Mercurial (hg). How to build UTGB from the source code. Install Mercurial (hg: 1.4.x or higher) and Maven (mvn command: 3.x or higher), then checkout the source code from the repository https:/ code.google.com/p/utgb/. Hosted at the google code. Hg clone https:/ code.google.com/p/utgb utgb $ cd utgb $ make clean install. Export PATH=$HOME/.utgb/bin;$PATH. Using a stable version. Developing UTGB with Eclipse. Auth] ...

2

UTGB Toolkit - Create Personalized Genome Browsers

http://utgenome.org/index.html

Create Personalized Genome Browsers with UTGB Toolkit. UTGB (University of Tokyo Genome Browser) Toolkit is an open-source software for developing personalized genome browsers that work in web browsers. UTGB Toolkit has following features:. UTGB uses AJAX-based web interfaces to avoid excessive reloading of web pages. The UTGB Toolkit is licensed under an open source license. And is freely available for both commercial and personal use. Create a your own genome browser. UTGB Toolkit User's Manual. This w...

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UTGB Toolkit -

http://utgenome.org/publication.html

UTGB Toolkit for Personalized Genome Browsers. Taro L. Saito, Jun Yoshimura, Shin Sasaki, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kuroshu and Shinichi Morishita. Bioinformatics. In press) (June 2009). Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites. MachiBase: A Drosophila Melanogaster 5'-end mRNA Transcription Database. ACM Portal http:/ doi.acm.org/10.1145/1376616.1376650. UTGB Medaka: Genomic Resource Database for Medaka Biology.

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UTGB Toolkit 1.5.1-SNAPSHOT Reference

http://utgenome.org/xref

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UTGB Toolkit -

http://utgenome.org/medaka

UTGB Medaka Genome Browser. Browser is available: http:/ utgenome.org/UTGBMedaka. Paste in your query sequence to find its location on the genomic sequences of specified species and revision. The online mapping system returns the locations found by BLAT alignment. The system accepts nucleotide sequences in the FASTA format or one flat string as input. Only sequences of length 18 - 100,000 bases will be processed. Assembled contigs (ver. 2). News and Recent Changes. The version 1.0. TIGR Medaka Gene Index.

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wormtss.utgenome.org

WormTSS: The Primary Transcriptome of C.elegans

http://wormtss.utgenome.org/browser/AllTSSList

Powerd by UTGB Toolkit.

wormtss.utgenome.org

WormTSS: The Primary Transcriptome of C.elegans

http://wormtss.utgenome.org/browser/download.jsp

Embryo TSS list (Excel) - 2013 Mar. Adult TSS list (Excel) - 2013 Mar. 5'SAGE Illumina single-end read (76bp). Embryo: read alignment BAM file. TSS peak data WIG file. Adult: read alignment BAM file. TSS peak data WIG file. 5'SAGE Illumina paired-end read (76bp-76bp). Embryo: read alignment BAM file. All raw reads are available in SRA ( SRA060670. Browsing with UCSC Genome Browser. To browse raw reads in UCSC Genome Browser, visit Manage Custom Tracks. With chromosome names I, II, ., etc.

trac.utgenome.org

UTGB - Trac

http://trac.utgenome.org/project/UTGB

UTGB Medaka http:/ utgenome.org/UTGBMedaka/. UTGB User Discussion Group. Welcome to Trac 0.10.3. Trac is a minimalistic. Management of software projects. Its goal is to simplify effective tracking and handling of software issues, enhancements and overall progress. All aspects of Trac have been designed with the single goal to help developers write great software. While staying out of the way. And imposing as little as possible on a team's established process and culture. You can use trac-admin.

wormtss.utgenome.org

WormTSS: The Primary Transcriptome of C.elegans

http://wormtss.utgenome.org/browser/browser.jsp

Use cursor key left/right to scroll horizontally, up: zoom out, down: zoom in. Powerd by UTGB Toolkit.

xerial.org

Taro L. Saito, Ph.D. | xerial.org

http://xerial.org/leo

Taro L. Saito. Taro L. Saito, Ph.D. Software Engineer at Treasure Data, Inc. Language Skills: Scala (current favorite), Java, C/C , Ruby, Perl, R, Scheme, OCaml, Z80, etc. GitHub https:/ github.com/xerial. BitBucket https:/ bitbucket.org/xerial. Tutorial of the Scala programming language. Presentation Slides @ SlideShare. Leo's Chronicle (in Japanese): http:/ leoclock.blogspot.com. Xerial Blog: http:/ voice.xerial.org. April 2005 - March 2007. April 2007 - February 2014. March 2014 - June 2015. MachiBase...

xerial.org

Genome Sciences | xerial.org

http://xerial.org/genome-science

Taro L. Saito. Cluser Computing Platform for Genome Sciences. Personal genome analysis involves massive amount of data analysis: genome sequence alignment, SNP calls, finding desease-related mutations, etc. These data analysis involves tons of data managment (e.g., compression, file I/O, table joins, filtering, etc.) Silk supports running these complex data analysis pipeline in a cluster machine. Genome browsers developed by UTGB. The Primary Transcriptome of. This is due to the high frequency of trans-s...

xerial.org

Publications | xerial.org

http://xerial.org/publication

Taro L. Saito. Taro L. Saito. Toshiya Nishimura, Amaury Herpin, Tetsuaki Kimura, Ikuyo Hara, Toshihiro Kawasaki, Shuhei Nakamura, Yasuhiro Yamamoto, Taro L. Saito. Jun Yoshimura, Shinichi Morishita, Tatsuya Tsukahara, Satoru Kobayashi, Kiyoshi Naruse, Shuji Shigenobu, Noriyoshi Sakai, Manfred Schartl, and Minoru Tanaka. Analysis of a novel gene, Sdgc, reveals sex chromosome-dependent differences of medaka germ cells prior to gonad formation. July 30, 2014, doi:10.1242/dev.106864. Taro L. Saito. Matthias ...

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utgenome.org

UTGB Toolkit - Create Personalized Genome Browsers

Create Personalized Genome Browsers with UTGB Toolkit. UTGB (University of Tokyo Genome Browser) Toolkit is an open-source software for developing personalized genome browsers that work in web browsers. UTGB Toolkit has following features:. UTGB uses AJAX-based web interfaces to avoid excessive reloading of web pages. The UTGB Toolkit is licensed under an open source license. And is freely available for both commercial and personal use. Create a your own genome browser. UTGB Toolkit User's Manual. This w...

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