Journal Article

Virtual-SAGE: A New Approach to EST Data Analysis

Valeriy Poroyko, Vladimir Calugaru, Mark Fredricksen and Hans J. Bohnert

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 11, issue 2, pages 145-152
Published in print January 2004 | ISSN: 1340-2838
Published online January 2004 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/11.2.145

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We present a computer program, termed V-SAGE (Virtual-SAGE), designed to facilitate the analysis of gene expression profiles by combining elements of SAGE (Serial Analysis of Gene Expression) with high-throughput EST analysis. The program re-iteratively correlates sequence tags adjacent to poly(A) tail sequence strings with a second or several tags located within the cDNA adjacent to the recognition sequences of frequently-cutting endonucleases. By recording tags and their distance, the program generates an expression profile from large numbers of sequences, groups sequences according to tags, and identifies alternatively spliced transcripts as well as transcripts that are characterized by 3′-UTR sequences of different length. We discuss the application of V-SAGE to a collection of corn root segment transcripts.

Keywords: Virtual-SAGE; alternative splicing; transcript 3′-end variation; high-throughput EST analysis; software

Journal Article.  0 words. 

Subjects: Genetics and Genomics

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