Expressed Sequence Tags (ESTs): Generation and Analysis

ISBN-13: 9781588297594 / Angielski / Twarda / 2009 / 332 str.

Parkinson, John

Opis

* Essential reading for any scientist beginning their own EST project * Takes the reader through the entire process of how to successfully complete an EST project * Covers a wide range of cDNA library construction techniques from the generation of full length libraries to the use of splice leaders and normalization and subtraction procedures * Details state-of-the-art bioinformatics pipelines and tools that can be readily implemented for high throughput processing and analysis of ESTs * Shows the reader how EST technology can be exploited for expression studies, particularly from the perspective of human health * Provides strategies, tips and potential pitfalls in the generation and analysis of ESTs from leading exponents of the field Over the past two decades, expressed sequence tags (ESTs - single pass reads from randomly selected cDNAs), have proven to be a remarkably cost-effective route for the purposes of gene discovery. Gaining in popularity, millions of ESTs have now been generated for over a thousand different species. In Expressed Sequence Tags (ESTs): Generation and Analysis, leading experts in the field introduce the reader to many of the fundamental concepts underlying the generation and analysis of ESTs through readily accessible and affordable sequencing technologies. The volume focuses on various methods used to generate, process and analyze EST datasets, while also exploring the use of EST technology for other purposes such as expression profiling, analysis of alternative transcripts, and phylogenomics. Written in the highly successful Methods in Molecular BiologyT series format, chapters include brief introductions to their respective topics, lists of the necessary materials and programs, step-by-step, readily reproducible protocols, and Notes sections, which highlight tips on troubleshooting and avoiding known pitfalls. Cutting-edge and easy to use, Expressed Sequence Tags (ESTs): Generation and Analysis serve

Spis treści

1. Expressed Sequence Tags: An Overview John Parkinson and Mark Blaxter 2. Strategies for Undertaking Expressed Sequence Tag (EST) Projects Sandra W. Clifton and Makedonka Mitreva 3. Construction of cDNA Libraries: Focus on Protists and Fungi Naiara Rodríguez-Ezpeleta, Shona Teijeiro, Lise Forget, Gertraud Burger and B. Franz Lang 4. Generation of Full-Length cDNA Libraries: Focus on Plants Motoaki Seki, Asako Kamiya, Piero Carninci, Yoshihide Hayashizaki, and Kazuo Shinozaki 5. Preparation of Full-Length cDNA Libraries: Focus on Metazoans Masako Harada and Yoshihide Hayashizaki 6. Expressed Sequence Tags: Normalization and Subtraction of cDNA Libraries Marcelo Bento Soares, Maria de Fatima Bonaldo, Jeremiah D. Hackett, and Debashish Bhattacharya 7. Generating EST Libraries: Trans-Spliced cDNAs Cecilia Fernández and Rick M. Maizels 8. Large-Scale Sequencing and Analytical Processing of ESTs Makedonka Mitreva and Elaine R. Mardis 9. EST Processing: From Trace to Sequence Ralf Schmid and Mark Blaxter 10. Obtaining Accurate Translations from Expressed Sequence Tags James Wasmuth and Mark Blaxter 11. EST Databases and Web Tools for EST Projects Yao-Qing Shen, Emmet O’Brien, Liisa Koski, B. Franz Lang, and Gertraud Burger 12. Phylogenomic Analysis of EST Datasets José M. Peregrín-Alvarez and John Parkinson 13. Statistical Analysis of Expressed Sequence Tags Edward Susko and Andrew J. Roger 14. Application of ESTs in Microarray Analysis Weizhong Li, Lisa Olohan, Daryl Williams, Margaret Hughes, Andrew Gracey, and Andrew Cossins 15. Exploiting ESTs in Human Health Sandro José de Souza

Blurb

Over the past two decades, expressed sequence tags (ESTs - single pass reads from randomly selected cDNAs), have proven to be a remarkably cost-effective route for the purposes of gene discovery. Gaining in popularity, millions of ESTs have now been generated for over a thousand different species. In Expressed Sequence Tags (ESTs): Generation and Analysis, leading experts in the field introduce the reader to many of the fundamental concepts underlying the generation and analysis of ESTs through readily accessible and affordable sequencing technologies. The volume focuses on various methods used to generate, process and analyze EST datasets, while also exploring the use of EST technology for other purposes such as expression profiling, analysis of alternative transcripts, and phylogenomics. Written in the highly successful Methods in Molecular Biology™ series format, chapters include brief introductions to their respective topics, lists of the necessary materials and programs, step-by-step, readily reproducible protocols, and Notes sections, which highlight tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and easy to use, Expressed Sequence Tags (ESTs): Generation and Analysis serves as an ideal reference for scientists continuing the vital investigation of genes and the genome.