Expressed sequence tag (EST), molecular marker
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This document discusses expressed sequence tags (ESTs), which are short sequences of cDNA used to identify genes and study gene expression. It provides a brief history of ESTs, noting they were first coined in 1991. ESTs are generated by sequencing fragments of cDNA from mRNA. They provide a quick and inexpensive way to discover new genes and study transcriptomes. Large databases of ESTs exist that can be searched and mined for various applications, including gene discovery, similarity searching, and transcriptome analysis. Pre-processing and clustering/assembling tools are used to improve EST data quality.
![MOLECULAR MARKER
EXPRESSED SEQUENCE TAGS [EST]
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )](https://image.slidesharecdn.com/expressedsequencetagsest-200510110634/85/Expressed-sequence-tag-EST-molecular-marker-1-320.jpg)
Expressed sequence tag (EST), molecular marker
- 1. MOLECULAR MARKER EXPRESSED SEQUENCE TAGS [EST] By KAUSHAL KUMAR SAHU Assistant Professor (Ad Hoc) Department of Biotechnology Govt. Digvijay Autonomous P. G. College Raj-Nandgaon ( C. G. )
- 2. SYNOPSIS Introduction History Why EST ? Generation of EST Errors associated with EST generation Improving EST EST data sources Application Conclusion Reference 2 E x p r e s s e d S e q u e n c e T a g s
- 3. INTRODUCTION Principle: The idea of ESTs generation is to sequence bits of DNA that represent genes expressed in certain cells, tissues, or organs from different organisms and use these "tags" to fish a gene out of a portion of chromosomal DNA by matching base pairs 3 E x p r e s s e d S e q u e n c e T a g s
- 4. HISTORY In 1991 the term expressed sequence tags (ESTs) was coined by Anthony Kerlavage at the Institute for Genomic Research. In 1991, Mark Adams used EST in relation to gene discovery and Human Genome project (led by Craig Venter). In 1992 dbEST was established as a division in Genbank. 4 E x p r e s s e d S e q u e n c e T a g s Mark Adams
- 5. WHY USE EST? EST collections are a relatively quick and inexpensive route for discovering new genes (Bourdon et al., 2002; Rogaev et al., 1995), Confirm coding regions in genomic sequence (Adams et al., 1991) Facilitate the construction of genome maps (Paterson et al., 2000), Can sometimes be interpreted directly for transcriptome activity (Ewing et al., 1999; Ogihara et al., 2003;Ronninget al., 2003) In addition, high-throughput technology and EST sequencing projects results in identification of significant portions of an organism’s gene content and thus can serve as a foundation for initiating genome sequencing projects (van der Hoeven et al., 2002). 5 E x p r e s s e d S e q u e n c e T a g s
- 7. Improving EST • Pre-processing: Softwares : Repeat Masker, Phred, Vectorstrip, UniVec etc • Clustering and Assembling: Softwares for clustering and assembling: CAP3, Phrap, stackPACK etc 7 E x p r e s s e d S e q u e n c e T a g s
- 8. Resources for EST data 8 E x p r e s s e d S e q u e n c e T a g s
- 9. APPLICATIONS EST as genome landmark Gene discovery Similarity searching Gene structure prediction Transcriptome analysis 9 E x p r e s s e d S e q u e n c e T a g s
- 10. REFERENCE A hitchhiker’s guide to expressed sequence tag (EST) analysis - Shivashankar H. Nagaraj, Robin B.Gasser and Shoba Ranganathan , 24th April 2006 – Vol. 8 p.no: 6-21 Site - http://bib.oxfordjournals.org Expressed sequence tags for genes: a review by François Hatey Gwenola Tosser-Klopp, Catherine Clouscard-Martinato Philippe Mulsant, François Gasser, Vol. 30, p.no. 521-541. Expressed sequence tags, Revised: March 29, 2004 site - http://www.ncbi.nlm.nih.gov/About/primer/est.html GENE CLONING AND DNA ANALYSIS: An Introduction Sixth Edition by T.A. BROWN 10 E x p r e s s e d S e q u e n c e T a g s