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


CONCLUSIONS
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.
Smith
Robin P
RP
The Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, USA. rsmith@med.miami.edu
Buchser
William J
WJ
Lemmon
Marcus B
MB
Pardinas
Jose R
JR
Bixby
John L
JL
Lemmon
Vance P
VP
D000465:Algorithms; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D016247:Information Storage and Retrieval / Q000379:methods; D012333:RNA, Messenger / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D012333:RNA, Messenger