Incidence of quasi-ditags in catalogs generated by Serial Analysis of Gene Expression SAGEReportar como inadecuado




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BMC Bioinformatics

, 5:152

First Online: 18 October 2004Received: 27 May 2004Accepted: 18 October 2004

Abstract

BackgroundSerial 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-.

ResultsWe 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.

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

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-5-152 contains supplementary material, which is available to authorized users.

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Autor: Sergey V Anisimov - Alexei A Sharov

Fuente: https://link.springer.com/



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