Tools & Service of RISe

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Tools & Service of RISe

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	RePS (repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. The updated version of RePS incorporates some of the ideas introduced by Phusion on clustering.

	BGF (BGI Gene Finder), developed by the Gene Finding Team at BGI, is a program for gene identification in eukaryotic genomic DNA sequences. It is based on Dynamic Programming and HSMM (Hidden Semi-Markov Model) algorithm with a special emphasis on rice genomes.(Mirror in Fudan University)


	Blast (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. It is more than a tool to view sequences aligned with each other or to calculate percent homology, but a program to locate regions of sequence similarity with a view to comparing structure and function.

	Blat is an accurate tool for analyzing vertebrate genomes. It is 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. It was developed by the Department of Biology and Center for Molecular Biology of RNA, University of California-Santa Cruz.

BGI Last Modified 2 Oct, 2003 Feedback _
Supported by China National Grid Project 2002AA104250