Friday, July 4, 2025 7/4/2025

Development and Maintenance of RepeatMasker and RepeatModeler

Award Number: R01HG002939
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 02/04/2022
PERIOD OF PERFORMANCE END DATE: 01/31/2027

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Development and Maintenance of RepeatMasker and RepeatModeler - Project Summary Mammalian and most other eukaryotic genomes contain a large number of interspersed repeats (IRs), most of which are copies of transposable elements (TEs) at varying levels of decay. Their presence complicates many genome sequence analyses, but their accurate identification in an early analysis stage can reduce these complications. In addition to their pervasiveness, over the last decades the research community has become widely familiar with their enormous impact on genome activity and evolution. Every species has been exposed to a unique, complex set of TEs leaving recognizable copies from as long ago as 300 million years to as recently as the present day. These TEs are uncovered and reconstructed by de novo discovery methods, often by our RepeatModeler tool, while their copies are then annotated by our RepeatMasker software. De novo methods can create TE libraries at a reasonable pace, but the product is far from the desired quality that can be reached by hand curation. With the recent explosive growth in sequenced species, these finishing steps, perhaps never fully automatable, now form a severe bottleneck in genome analyses due to a lack of manpower and expertise, while the results, especially when produced by different methods from different research groups, lack consistency and suffer from redundancy. Furthermore, the annotation of genomes for which high-quality libraries have been created is not keeping up with library improvements due to the computational burden of re-analysis. In this proposal, we describe a plan to refactor RepeatMasker by generalizing and improving TE alignment adjudication, switching to a family-centric search strategy with support for incremental re-analysis, improving annotation reporting and supporting cluster environments. Responding to the need for improved methods for automated TE library generation we propose making significant changes to RepeatModeler’s core discovery algorithms, develop a novel model extension tool, and. In addition, we will extend our novel methods for exploiting multi-species alignments and ancestral reconstructions and utilize them to build a comprehensive mammalian TE library.


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: 2025 ( Subtotal = $591,186 )
2025	2025	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	001	19	4/25/2025	NON-COMPETING CONTINUATION	$59,119
2025	2025	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	19	4/9/2025	NON-COMPETING CONTINUATION	$532,067
														Subtotal = $591,186

Issue Date FY: 2024 ( Subtotal = $576,412 )
2024	2024	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	001	18	7/11/2024	NON-COMPETING CONTINUATION	$47,055
2024	2024	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	18	2/22/2024	NON-COMPETING CONTINUATION	$529,357
														Subtotal = $576,412

Issue Date FY: 2023 ( Subtotal = $588,173 )
2023	2023	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	17	3/1/2023	NON-COMPETING CONTINUATION	$588,173
														Subtotal = $588,173

Issue Date FY: 2022 ( Subtotal = $532,405 )
2022	2022	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	002	16	5/3/2022	COMPETING CONTINUATION	$1,588
2022	2022	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	16	2/4/2022	COMPETING CONTINUATION	$532,405
2022	2020	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	001	15	5/3/2022	NON-COMPETING CONTINUATION	-$1,588
														Subtotal = $532,405

Issue Date FY: 2020 ( Subtotal = $490,561 )
2020	2020	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	15	3/23/2020	NON-COMPETING CONTINUATION	$490,561
														Subtotal = $490,561

Issue Date FY: 2019 ( Subtotal = $498,796 )
2019	2019	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	001	14	4/2/2019	NON-COMPETING CONTINUATION	$498,796
2019	2016	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	12	3/29/2019	NON-COMPETING CONTINUATION	$0
														Subtotal = $498,796

Issue Date FY: 2018 ( Subtotal = $497,986 )
2018	2018	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	13	4/30/2018	COMPETING CONTINUATION	$497,986
														Subtotal = $497,986

Issue Date FY: 2016 ( Subtotal = $457,500 )
2016	2016	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	12	3/30/2016	NON-COMPETING CONTINUATION	$457,500
														Subtotal = $457,500

Issue Date FY: 2015 ( Subtotal = $446,062 )
2015	2015	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	11	4/18/2015	NON-COMPETING CONTINUATION	$446,062
														Subtotal = $446,062

Issue Date FY: 2014 ( Subtotal = $457,500 )
2014	2014	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	001	10	5/9/2014	COMPETING CONTINUATION	$450,001
2014	2014	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	002	10	7/23/2014	COMPETING CONTINUATION	$7,499
2014	2012	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	9	11/8/2013	NON-COMPETING CONTINUATION	$0
														Subtotal = $457,500

Issue Date FY: 2012 ( Subtotal = $397,684 )
2012	2012	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	9	3/21/2012	NON-COMPETING CONTINUATION	$397,684
														Subtotal = $397,684

Issue Date FY: 2011 ( Subtotal = $397,684 )
2011	2011	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	001	8	5/19/2011	NON-COMPETING CONTINUATION	$36,153
2011	2011	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	8	3/3/2011	NON-COMPETING CONTINUATION	$361,531
														Subtotal = $397,684

Issue Date FY: 2010 ( Subtotal = $390,000 )
2010	2010	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	7	2/12/2010	COMPETING CONTINUATION	$390,000
2010	2008	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	001	6	2/12/2010	NON-COMPETING CONTINUATION	$0
														Subtotal = $390,000

Issue Date FY: 2008 ( Subtotal = $361,970 )
2008	2008	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	6	6/30/2008	NON-COMPETING CONTINUATION	$361,970
														Subtotal = $361,970

Issue Date FY: 2007 ( Subtotal = $368,980 )
2007	2007	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	5	6/29/2007	NON-COMPETING CONTINUATION	$368,980
														Subtotal = $368,980

Issue Date FY: 2006 ( Subtotal = $380,000 )
2006	2006	INSTITUTE FOR SYSTEMS BIOLOGY	1441 N 34TH STREET	SEATTLE	WA	98103	KING	USA	Human Genome Research	000	4	9/21/2006	COMPETING CONTINUATION	$380,000
														Subtotal = $380,000

Issue Date FY: 2005 ( Subtotal = $352,000 )
2005	2005	INSTITUTE FOR SYSTEMS BIOLOGY	4225 ROOSEVELT WAY NORTHEAST	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	3	6/30/2005	NON-COMPETING CONTINUATION	$352,000
														Subtotal = $352,000

Issue Date FY: 2004 ( Subtotal = $352,000 )
2004	2004	INSTITUTE FOR SYSTEMS BIOLOGY	4225 ROOSEVELT WAY NORTHEAST	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	2	6/23/2004	NON-COMPETING CONTINUATION	$352,000
														Subtotal = $352,000

Issue Date FY: 2003 ( Subtotal = $352,000 )
2003	2003	INSTITUTE FOR SYSTEMS BIOLOGY	4225 ROOSEVELT WAY NORTHEAST	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	1	8/7/2003	NEW	$352,000
														Subtotal = $352,000

Grand Total All Awards = $8,488,899

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Development and Maintenance of RepeatMasker and RepeatModeler

Award Number: R01HG002939

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 02/04/2022

PERIOD OF PERFORMANCE END DATE: 01/31/2027

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