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COMPUTATIONAL GENE MODELING AND GENOME SEQUENCE ASSEMBLY

Award Number: R01LM006845
ORGANIZATION: NATIONAL LIBRARY OF MEDICINE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/01/2009
PERIOD OF PERFORMANCE END DATE: 06/30/2011

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COMPUTATIONAL GENE MODELING AND GENOME SEQUENCE ASSEMBLY - DESCRIPTION (provided by applicant): This project addresses two major bioinformatics problems: the development of better software for finding genes in eukaryotic genome sequences, and the development of genome assemblers for large shotgun sequencing projects. The gene finding project will pursue two tracks: first, we will continue to improve our Generalized Hidden Markov Model and our Pair Hidden Markov Model gene finders, training them for new species as new genomes appear, and enhancing their capabilities to use related species as a guide to gene finding in a new species. Second, we will develop a new eukaryotic annotation pipeline, which will integrate the results from a wide range of sources, including gene finders, protein sequence alignments, cDNA and EST alignments, and other sequence features. This pipeline will be used to predict comprehensive gene sets for multiple species, focusing especially on species for which the available annotation is incomplete or outdated. The pipeline will also be available as a service to annotate genomes for other groups. The assembler project will include several major efforts. First, we will continue to build on our successful open source assembler project, AMOS, adding new modules to allow inter-operation with other assembly packages. Second, we will develop new assemblers that can handle pyrosequencing data, low coverage genome projects, and sequences collected from complex mixtures of species. Third, we will provide assembly services to genome sequencing centers and other collaborators, helping them to assemble genomes using the latest available assembly tools. These will include new sequencing projects as well as genomes that, although already sequenced, can be re-assembled more accurately using improved assembly software. For all of the software development projects, we will continue our practice of making all our source code freely available to investigators in the scientific research community worldwide.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2011 ( Subtotal = $0 )
2011	2010	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Medical Library Assistance	001	11	9/20/2011	NON-COMPETING CONTINUATION	$0
2011	2009	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Trans-NIH Recovery Act Research Support	000	10	12/29/2010	SUPPLEMENT FOR EXPANSION	$0
2011	2009	JOHNS HOPKINS UNIVERSITY, SCHOOL OF MEDICINE	720 RUTLAND AVENUE	BALTIMORE	MD	21205	BALTIMORE CITY	USA	Trans-NIH Recovery Act Research Support	002	10	9/28/2011	SUPPLEMENT FOR EXPANSION	$109,006
2011	2009	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Trans-NIH Recovery Act Research Support	003	10	9/28/2011	SUPPLEMENT FOR EXPANSION	-$109,006
														Subtotal = $0

Issue Date FY: 2010 ( Subtotal = $608,513 )
2010	2010	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Medical Library Assistance	000	11	5/24/2010	NON-COMPETING CONTINUATION	$608,513
														Subtotal = $608,513

Issue Date FY: 2009 ( Subtotal = $853,620 )
2009	2009	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Medical Library Assistance	000	10	6/2/2009	NON-COMPETING CONTINUATION	$603,620
2009	2009	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Trans-NIH Recovery Act Research Support	001	10	7/17/2009	SUPPLEMENT FOR EXPANSION	$250,000
														Subtotal = $853,620

Issue Date FY: 2008 ( Subtotal = $588,371 )
2008	2008	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Medical Library Assistance	000	9	5/30/2008	NON-COMPETING CONTINUATION	$588,371
														Subtotal = $588,371

Issue Date FY: 2007 ( Subtotal = $556,536 )
2007	2007	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Medical Library Assistance	000	8	6/1/2007	COMPETING CONTINUATION	$556,536
														Subtotal = $556,536

Issue Date FY: 2005 ( Subtotal = $671,899 )
2005	2005	UNIVERSITY OF MARYLAND	1410 SERVICE BUILDING	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Medical Library Assistance	000	7	9/23/2005	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$596,899
2005	2005	UNIVERSITY OF MARYLAND	1410 SERVICE BUILDING	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Medical Library Assistance	001	7	9/26/2005	SUPPLEMENT FOR EXPANSION	$75,000
														Subtotal = $671,899

Issue Date FY: 2004 ( Subtotal = $671,976 )
2004	2004	INSTITUTE FOR GENOMIC RESEARCH (THE)	9712 MEDICAL CENTER DRIVE	ROCKVILLE	MD	20850	MONTGOMERY	USA	Medical Library Assistance	000	6	9/10/2004	NON-COMPETING CONTINUATION	$671,976
														Subtotal = $671,976

Issue Date FY: 2003 ( Subtotal = $652,539 )
2003	2003	INSTITUTE FOR GENOMIC RESEARCH (THE)	9712 MEDICAL CENTER DRIVE	ROCKVILLE	MD	20850	MONTGOMERY	USA	Medical Library Assistance	000	5	9/18/2003	NON-COMPETING CONTINUATION	$652,539
														Subtotal = $652,539

Issue Date FY: 2002 ( Subtotal = $706,406 )
2002	2002	INSTITUTE FOR GENOMIC RESEARCH (THE)	9712 MEDICAL CENTER DRIVE	ROCKVILLE	MD	20850	MONTGOMERY	USA	Medical Library Assistance	001	4	9/25/2002	SUPPLEMENT FOR EXPANSION	$60,192
2002	2002	INSTITUTE FOR GENOMIC RESEARCH (THE)	9712 MEDICAL CENTER DRIVE	ROCKVILLE	MD	20850	MONTGOMERY	USA	Indicates awards funded from multiple programs	000	4	9/23/2002	COMPETING CONTINUATION	$646,214
														Subtotal = $706,406

Issue Date FY: 2001 ( Subtotal = $322,047 )
2001	2001	INSTITUTE FOR GENOMIC RESEARCH (THE)	9712 MEDICAL CENTER DRIVE	ROCKVILLE	MD	20850	MONTGOMERY	USA	Medical Library Assistance	000	3	7/30/2001	NON-COMPETING CONTINUATION	$280,780
2001	2001	INSTITUTE FOR GENOMIC RESEARCH (THE)	9712 MEDICAL CENTER DRIVE	ROCKVILLE	MD	20850	MONTGOMERY	USA	Medical Library Assistance	001	3	9/13/2001	SUPPLEMENT FOR EXPANSION	$41,267
														Subtotal = $322,047

Issue Date FY: 2000 ( Subtotal = $272,127 )
2000	2000	INSTITUTE FOR GENOMIC RESEARCH (THE)	9712 MEDICAL CENTER DRIVE	ROCKVILLE	MD	20850	MONTGOMERY	USA	Medical Library Assistance	000	2	9/5/2000	NON-COMPETING CONTINUATION	$272,127
														Subtotal = $272,127

Issue Date FY: 1999 ( Subtotal = $267,416 )
1999	1999	INSTITUTE FOR GENOMIC RESEARCH (THE)	9712 MEDICAL CENTER DRIVE	ROCKVILLE	MD	20850	MONTGOMERY	USA	Medical Library Assistance	000	1	8/12/1999	NEW	$267,416
														Subtotal = $267,416

Grand Total All Awards = $6,171,450

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COMPUTATIONAL GENE MODELING AND GENOME SEQUENCE ASSEMBLY

Award Number: R01LM006845

ORGANIZATION: NATIONAL LIBRARY OF MEDICINE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 08/01/2009

PERIOD OF PERFORMANCE END DATE: 06/30/2011

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