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 g...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 9; no. 1; p. 186
Main Authors: Smith, Robin P, Buchser, William J, Lemmon, Marcus B, Pardinas, Jose R, Bixby, John L, Lemmon, Vance P
Format: Journal Article
Language:English
Published: London BioMed Central 10.04.2008
BioMed Central Ltd
BMC
Subjects:
Algorithms
Bioinformatics
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Databases, Genetic
Expressed Sequence Tags
Gene expression
Gene Expression Profiling - methods
Gene Library
Genomic libraries
Information Storage and Retrieval - methods
Life Sciences
Microarrays
Online databases
RNA, Messenger - genetics
Sequence Alignment - methods
Sequence Analysis, RNA - methods
Software
United States
Phred Score
UniGene Cluster
RefSeq Protein
Entrez Gene Database
Entrez Gene Identifier
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary: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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-9-186