ESTPiper – a web-based analysis pipeline for expressed sequence tags

The intuitive web interface guides users through each step of base calling, data cleaning, assembly, genome alignment, annotation, analysis of gene ontology (GO), and microarray oligonucleotide probe design. Each step is modularized. Therefore, a user can execute them separately or together in batch mode. In addition, the user has control over the parameters used by the underlying programs. Extensive documentation of ESTPiper's functionality is embedded throughout the web site to facilitate understanding of the required input and interpretation of the computational results. The user can also download intermediate results and port files to separate programs for further analysis. In addition, our server provides a time-stamped description of the run history for reproducibility. The pipeline can also be installed locally, allowing researchers to modify ESTPiper to suit their own needs.ESTPiper streamlines the typical process of EST analysis. The pipeline was initially designed in part to support the Daphnia pulex cDNA sequencing project. A web server hosting ESTPiper is provided at http://estpiper.cgb.indiana.edu/ webcite to now support projects of all size. The software is also freely available from the authors for local installations.Expressed sequence tags (ESTs) are generated by single-pass sequencing of complementary DNA (cDNA) [1]. Because ESTs correspond to the transcribed regions of a genome, EST sequencing has been a common strategy for gene discovery – especially for organisms with complex genomes. For example, many agriculturally important plants (e.g., sunflower, wheat) have enormous genomes containing many repetitive elements and large intergenic regions. For these taxa, EST sequencing remains (for now) the only efficient way to discover genes on genome-wide scale, since the repetitive elements still pose an unsolved challenge for whole genome assembly. Even for species with draft genome sequences, ESTs remain the gold standard for accurate gene structure