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

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

doi:10.1186/1471-2105-9-186

Robin P Smith, Jose R Pardinas + Show 4 more

Open Access

https://doi.org/10.1186/1471-2105-9-186

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Abstract

BackgroundSeveral 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.ResultsWe 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.ConclusionEST 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.

Highlights

Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed
Selection of appropriate Entrez Gene identifiers based on RefSeq links proved efficacious: only 23 sequences match Entrez Gene identifiers without a RefSeq link, allowing full-length analysis of 83% of samples returning a BLAST hit (Figure 3b)
We have developed a valuable new tool named EST Express for the identification, annotation and analysis of cDNA library sequences

Summary

Results

We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization

Conclusion

Background

Results and Discussion