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Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W459-62.

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.

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  • 1Laboratory of Bioknowledge Systems, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan. amasoudi@kais.kyoto-u.ac.jp

Abstract

Expressed sequence tag (EST) sequencing has proven to be an economically feasible alternative for gene discovery in species lacking a draft genome sequence. Ongoing large-scale EST sequencing projects feel the need for bioinformatics tools to facilitate uniform EST handling. This brings about a renewed importance for a universal tool for processing and functional annotation of large sets of ESTs. EGassembler (http://egassembler.hgc.jp/) is a web server, which 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 a unique all-in-one online application web service for large-scale ESTs and genomic DNA clustering and assembling. 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. The service provides an excellent bioinformatics tool to research groups in wet-lab as well as an all-in-one-tool for sequence handling to bioinformatics researchers.

PMID:
16845049
[PubMed - indexed for MEDLINE]
PMCID:
PMC1538775
Free PMC Article
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