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Open Access Methodology article

Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)

Sergey V Anisimov1* and Alexei A Sharov2

Author Affiliations

1 Section for Neuronal Survival, Wallenberg Neuroscience Center, Lund University, 221 84 Lund, Sweden

2 Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA

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BMC Bioinformatics 2004, 5:152  doi:10.1186/1471-2105-5-152

Published: 18 October 2004

Abstract

Background

Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries relies on the identification of ditags from sequencing files; however, the software used to examine SAGE libraries cannot distinguish between authentic versus false ditags ("quasi-ditags").

Results

We provide examples of quasi-ditags that originate from cloning and sequencing artifacts (i.e. genomic contamination or random combinations of nucleotides) that are included in SAGE libraries. We have employed a mathematical model to predict the frequency of quasi-ditags in random nucleotide sequences, and our data show that clones containing less than or equal to 2 ditags (which include chromosomal cloning artifacts) should be excluded from the analysis of SAGE catalogs.

Conclusions

Cloning and sequencing artifacts contaminating SAGE libraries could be eliminated using simple pre-screening procedure to increase the reliability of the data.