Literature DB >> 12651724

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

Geo Pertea1, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush.   

Abstract

TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including SMP and PVM.

Mesh：

Year:  2003        PMID： 12651724     DOI： 10.1093/bioinformatics/btg034

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  792 in total

1.  A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales.

Authors:  Joseph C Kuhl; Foo Cheung; Qiaoping Yuan; William Martin; Yayeh Zewdie; John McCallum; Andrew Catanach; Paul Rutherford; Kenneth C Sink; Maria Jenderek; James P Prince; Christopher D Town; Michael J Havey
Journal:  Plant Cell       Date:  2003-12-11       Impact factor: 11.277

2.  hRIP, a cellular cofactor for Rev function, promotes release of HIV RNAs from the perinuclear region.

Authors:  Nuria Sánchez-Velar; Enyeneama B Udofia; Zhong Yu; Maria L Zapp
Journal:  Genes Dev       Date:  2003-12-30       Impact factor: 11.361

3.  Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.

Authors:  Bastien Chevreux; Thomas Pfisterer; Bernd Drescher; Albert J Driesel; Werner E G Müller; Thomas Wetter; Sándor Suhai
Journal:  Genome Res       Date:  2004-05-12       Impact factor: 9.043

4.  Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish.

Authors:  Shufen Wang; Xiufeng Wang; Qiwei He; Xianxian Liu; Wenling Xu; Libin Li; Jianwei Gao; Fengde Wang
Journal:  Plant Cell Rep       Date:  2012-04-04       Impact factor: 4.570

5.  Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.

Authors:  Laura Wegener Parfrey; Jessica Grant; Yonas I Tekle; Erica Lasek-Nesselquist; Hilary G Morrison; Mitchell L Sogin; David J Patterson; Laura A Katz
Journal:  Syst Biol       Date:  2010-07-23       Impact factor: 15.683

Review 6.  A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp.

Authors:  Jiann-Horng Leu; Shu-Hwa Chen; Yu-Bin Wang; Yen-Chen Chen; Sheng-Yao Su; Chung-Yen Lin; Jan-Ming Ho; Chu-Fang Lo
Journal:  Mar Biotechnol (NY)       Date:  2010-04-17       Impact factor: 3.619

7.  Specific and shared targets of ephrin A signaling in epidermal keratinocytes.

Authors:  Rebecca Walsh; Miroslav Blumenberg
Journal:  J Biol Chem       Date:  2010-12-30       Impact factor: 5.157

8.  PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries.

Authors:  Hirohide Uenishi; Tomoko Eguchi; Kohei Suzuki; Tetsuya Sawazaki; Daisuke Toki; Hiroki Shinkai; Naohiko Okumura; Noriyuki Hamasima; Takashi Awata
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

9.  De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes.

Authors:  Hélène Hinaux; Julie Poulain; Corinne Da Silva; Céline Noirot; William R Jeffery; Didier Casane; Sylvie Rétaux
Journal:  PLoS One       Date:  2013-01-09       Impact factor: 3.240

10.  Proteomic identification and characterization of a novel peroxisomal adenine nucleotide transporter supplying ATP for fatty acid beta-oxidation in soybean and Arabidopsis.

Authors:  Yuko Arai; Makoto Hayashi; Mikio Nishimura
Journal:  Plant Cell       Date:  2008-12-10       Impact factor: 11.277
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.