EST express: PHP/MySQL based automated annotation of ESTs from expression libraries

Robin P. Smith, William J. Buchser, Marcus B. Lemmon, Jose R. Pardinas, John Bixby, Vance Lemmon

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results: We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. Conclusion: EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

Original languageEnglish
Article number186
JournalBMC Bioinformatics
Volume9
DOIs
StatePublished - Apr 10 2008

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Expressed Sequence Tags
Annotation
CDNA
Express
Genes
Gene
Software
Gene Library
Web Server
Graphical user interfaces
Large Data Sets
Yeast
Open Source
Messenger RNA
Sequencing
Engine
Servers
Complementary DNA
Yeasts
Research Personnel

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

EST express : PHP/MySQL based automated annotation of ESTs from expression libraries. / Smith, Robin P.; Buchser, William J.; Lemmon, Marcus B.; Pardinas, Jose R.; Bixby, John; Lemmon, Vance.

In: BMC Bioinformatics, Vol. 9, 186, 10.04.2008.

Research output: Contribution to journalArticle

Smith, Robin P. ; Buchser, William J. ; Lemmon, Marcus B. ; Pardinas, Jose R. ; Bixby, John ; Lemmon, Vance. / EST express : PHP/MySQL based automated annotation of ESTs from expression libraries. In: BMC Bioinformatics. 2008 ; Vol. 9.
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