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Abstract

Grant Number:	2R01LM006845-04
Project Title:	Computational Gene Modeling and Genome Sequence Assembly

PI Information:	Name	Email	Title
	SALZBERG, STEVEN L.	salzberg@umiacs.umd.edu	HORVITZ PROFESSOR OF COMPUTER SCIENCE

Abstract: DESCRIPTION (provided by applicant): This project will address two major bioinformatics problems: the development of new and improved software for finding genes in eukaryotic genome sequences, and the development of a sequence assembler that is capable of assembling very large genomes. The gene finding project will pursue three tracks: first, we will improve our existing eukaryotic gene finding system, GlimmerM, adding the ability to recognize new sequence patterns and enhancing the ease with which the system can be adapted to new organisms. Second, we will develop a new gene finder, based on Pair Hidden Markov Models (PHMMs), which will use the sequence similarity between two related organisms to find genes in both species simultaneously. Third, we will develop a system for integrating the output from multiple gene finders and from sequence alignment programs in order to produce gene models that incorporate all available evidence. The assembler project will include the development of several major components. The overall goal is to build a sequence assembler that will be able to assemble data from whole-genome shotgun sequencing projects for genomes ranging from a few million base pairs up to billions of base pairs. The assembler will have the ability to accept as input both raw sequencing reads and a mixture of reads and already-assembled sequences. A separate scaffold-building program will create larger scaffolds from a set of assemblies by using information from paired-end sequences. In addition, this project will develop and distribute a genome assembler benchmark set, containing sequences from shotgun sequencing projects for which the correct assembly is known. For all of the software development projects, the source code will be made freely available to investigators in the scientific research community worldwide.

Public Health Relevance:
This Public Health Relevance is not available.

Thesaurus Terms:
computer assisted sequence analysis, computer simulation, computer system design /evaluation, genome, molecular biology information system
DNA replication origin, genetic model, genetic translation, information retrieval, nucleic acid sequence, polyadenylate, species difference, spliceosome
statistics /biometry

Institution:	INSTITUTE FOR GENOMIC RESEARCH
	9712 MEDICAL CENTER DR
	ROCKVILLE, MD 20850
Fiscal Year:	2002
Department:
Project Start:	01-SEP-1999
Project End:	29-SEP-2006
ICD:	NATIONAL LIBRARY OF MEDICINE
IRG:	BLR

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