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

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 a

SUBMITTER: Anisimov SV 

PROVIDER: S-EPMC526221 | biostudies-literature | 2004 Oct

REPOSITORIES: biostudies-literature