bookmark EGassembler Aligns and merges sequence fragments resulting from shotgun sequencing or gene transcripts (expressed sequence tag (EST)) fragments in order to reconstruct the original segment or gene. EGassembler provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling of ESTs and genomic fragments. The web server is publicly available and provides the community an all-in-one online application web service. Running on a Sun Fire 15K supercomputer, a significantly large volume of data can be processed in a short period of time. The results can be used to functionally annotate genes, to facilitate splice alignment analysis, to link the transcripts to genetic and physical maps, design microarray chips, to perform transcriptome analysis and to map to KEGG metabolic pathways.