Book ChapterDOI
Expressed sequence tags: an overview.
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TLDR
This volume provides practical details on the generation and analysis of ESTs, which cover creation of cDNA libraries; generation and processing of sequence data; bioinformatics analysis ofESTs; and their application to phylogenetics and transcript profiling.Abstract:
Expressed sequence tags (ESTs) are fragments of mRNA sequences derived through single sequencing reactions performed on randomly selected clones from cDNA libraries. To date, over 45 million ESTs have been generated from over 1400 different species of eukaryotes. For the most part, EST projects are used to either complement existing genome projects or serve as low-cost alternatives for purposes of gene discovery. However, with improvements in accuracy and coverage, they are beginning to find application in fields such as phylogenetics, transcript profiling and proteomics. This volume provides practical details on the generation and analysis of ESTs. Chapters are presented which cover creation of cDNA libraries; generation and processing of sequence data; bioinformatics analysis of ESTs; and their application to phylogenetics and transcript profiling.read more
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Journal Article
Draft genome of the filarial nematode parasite Brugia malayi (Science (2007) (1756))
TL;DR: Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during ∼350 million years of evolution, they largely remain in linkage on chromosomal units.
Journal ArticleDOI
De Novo Sequencing and Analysis of the American Ginseng Root Transcriptome Using a GS FLX Titanium Platform to Discover Putative Genes Involved in Ginsenoside Biosynthesis
Chao Sun,Ying Li,Qiong Wu,Hongmei Luo,Yongzhen Sun,Jingyuan Song,Edmund M.K. Lui,Shilin Chen +7 more
TL;DR: It is demonstrated that transcriptome analysis based on 454 pyrosequencing is a powerful tool for determining the genes encoding enzymes responsible for the biosynthesis of secondary metabolites in non-model plants.
Journal ArticleDOI
Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers.
Hongmei Luo,Chao Sun,Yongzhen Sun,Qiong Wu,Ying Li,Jingyuan Song,Yunyun Niu,Xiang-lin Cheng,Hong-Xi Xu,Chuyuan Li,Juyan Liu,André Steinmetz,Shilin Chen +12 more
TL;DR: This study is the first to present a large-scale EST dataset for P. notoginseng root acquired by next-generation sequencing (NGS) technology and establishes an important foundation for the study with the purpose of ensuring adequate drug resources for this species.
Journal ArticleDOI
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery
TL;DR: An increasing number of large-scale genetic variant discovery initiatives are being undertaken in conjunction with next-generation sequencing platforms, allowing for drastically quicker and cheaper variant discovery, and leading towards a far more comprehensive view of the genome or transcriptome.
Journal ArticleDOI
The Complete Mitochondrial Genome and Novel Gene Arrangement of the Unique-Headed Bug Stenopirates sp. (Hemiptera: Enicocephalidae)
TL;DR: The mitochondrial genome of the unique-headed bug Stenopirates sp.
References
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Profile hidden Markov models.
TL;DR: Profile HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise and complement standard pairwise comparison methods for large-scale sequence analysis.
Journal ArticleDOI
Complementary DNA sequencing : expressed sequence tags and human genome project
Mark Raymond Adams,Jenny M. Kelley,Jeannine D. Gocayne,Mark Dubnick,Mihael H. Polymeropoulos,Hong Xiao,Carl R. Merril,Andrew Wu,Bjorn Olde,Ruben F. Moreno,Anthony R. Kerlavage,W. Richard McCombie,J. Craig Venter +12 more
TL;DR: Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs), which will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing.
Journal ArticleDOI
dbEST — database for “expressed sequence tags”
Journal ArticleDOI
Database resources of the National Center for Biotechnology
David L. Wheeler,Deanna M. Church,Scott Federhen,Alex E. Lash,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tatiana Tatusova,Lukas Wagner +10 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site.
Journal ArticleDOI
Draft Genome of the Filarial Nematode Parasite Brugia malayi
Elodie Ghedin,Elodie Ghedin,Shiliang Wang,David J. Spiro,Elisabet Caler,Qi Zhao,Jonathan Crabtree,Jonathan E. Allen,Arthur L. Delcher,David B. Guiliano,Diego Miranda-Saavedra,Samuel V. Angiuoli,Todd Creasy,Paolo Amedeo,Brian J. Haas,Najib M. El-Sayed,Jennifer R. Wortman,Tamara Feldblyum,Luke J. Tallon,Michael C. Schatz,Martin Shumway,Hean Koo,Steven L. Salzberg,Seth Schobel,Mihaela Pertea,Mihai Pop,Owen White,Geoffrey J. Barton,Clotilde K. S. Carlow,Crawford Michael J,Jennifer Daub,Dimmic Matt W,Chris F. Estes,Jeremy M. Foster,Mehul B. Ganatra,William F. Gregory,Nicholas M. Johnson,Jinming Jin,Richard Komuniecki,Ian F Korf,Sanjay Kumar,Sandra J. Laney,Ben-Wen Li,Wen Li,Tim H. Lindblom,Sara Lustigman,Dong Ma,Claude V. Maina,David M. A. Martin,James P. McCarter,Larry A. McReynolds,Makedonka Mitreva,Thomas B. Nutman,John Parkinson,José M. Peregrín-Alvarez,Catherine B. Poole,Qinghu Ren,Lori Saunders,Ann E. Sluder,Katherine A. Smith,Mario Stanke,Thomas R. Unnasch,Jenna Ware,Aguan Wei,Gary J. Weil,Deryck J. Williams,Yinhua Zhang,Steven A. Williams,Claire M. Fraser-Liggett,Barton E. Slatko,Mark Blaxter,Alan L. Scott +71 more
TL;DR: In this article, the authors sequenced the ∼90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predicted ∼11,500 protein coding genes in 71 Mb of robustly assembled sequence.
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