Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data.

BMC Biotechnology
Sun ZhouChun Liang

Abstract

Expressed Sequence Tag (EST) sequences are widely used in applications such as genome annotation, gene discovery and gene expression studies. However, some of GenBank dbEST sequences have proven to be "unclean". Identification of cDNA termini/ends and their structures in raw ESTs not only facilitates data quality control and accurate delineation of transcription ends, but also furthers our understanding of the potential sources of data abnormalities/errors present in the wet-lab procedures for cDNA library construction. After analyzing a total of 309,976 raw Pinus taeda ESTs, we uncovered many distinct variations of cDNA termini, some of which prove to be good indicators of wet-lab artifacts, and characterized each raw EST by its cDNA terminus structure patterns. In contrast to the expected patterns, many ESTs displayed complex and/or abnormal patterns that represent potential wet-lab errors such as: a failure of one or both of the restriction enzymes to cut the plasmid vector; a failure of the restriction enzymes to cut the vector at the correct positions; the insertion of two cDNA inserts into a single vector; the insertion of multiple and/or concatenated adapters/linkers; the presence of 3'-end terminal structures in designa...Continue Reading

References

Feb 13, 1992·Nature·M D AdamsJ C Venter
Sep 1, 1996·Genome Research·L D HillierM Marra
Dec 26, 2001·Bioinformatics·H H Chou, M H Holmes
Nov 14, 2003·Genome Research·Melody S ClarkStephen L Johnson
May 8, 2004·Bioinformatics·Song Li, Hui-Hsien Chou
Jul 21, 2004·Bioinformatics·Tim BeissbarthTerence P Speed
Apr 12, 2005·Plant Molecular Biology·Nathalie PavyJohn Mackay
May 10, 2007·Nucleic Acids Research·Chun LiangJeffrey F D Dean

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Citations

Sep 21, 2012·Plant Physiology·Zinnia Haydee González-CarranzaJeremy Alan Roberts
Jun 21, 2014·Molecular Genetics and Genomics : MGG·Chunxian ChenTom G Beckman

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Methods Mentioned

BETA
cDNA
cDNA library construction
cDNA library

Software Mentioned

AFST
SQLite
UGALGB
Lucy
MySQL
SeqClean

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