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Dfam: sustainable growth, curation support, and improved quality for mobile element annotation

Award Number: U24HG010136
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/15/2018
PERIOD OF PERFORMANCE END DATE: 06/30/2028

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Dfam: sustainable growth, curation support, and improved quality for mobile element annotation - Project Summary / Abstract Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Thorough and accurate annotation of repetitive content in genomes depends on a comprehensive database of known TEs, along with robust statistical and procedural methods for recognizing decayed instances of elements and disentangling their complex relationships. Annotation of TE instances is usually performed using our RepeatMasker software, which compares a genome to a database containing representations of known repeat families. These have historically been consensus sequences, which generally approximate the sequences of the original TEs. Our Dfam database is an open access collection of repetitive DNA families, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). We have demonstrated that profile HMMs support improved annotation sensitivity, and Dfam provides numerous aids to both curators of TE families and those who make use of the resulting annotations. During the life of this grant, the database has grown to include families belonging to more than 1000 species (from a baseline of 5). This growth has introduced a number of scale-based pressures, which in some cases have forced us to reduce Dfam functionality in response, and in other cases highlighted ways that the resource can better meet the needs of the community. Our proposed efforts largely target these matters while continuing to expand and diversify the resource.


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 = $529,832 )
2025	2025	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	8	8/9/2025	NON-COMPETING CONTINUATION	$529,832
														Subtotal = $529,832

Issue Date FY: 2024 ( Subtotal = $529,832 )
2024	2024	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	004	7	9/24/2024	NON-COMPETING CONTINUATION	$0
2024	2024	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	003	7	8/5/2024	NON-COMPETING CONTINUATION	$529,832
2024	2023	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	002	6	3/14/2024	COMPETING CONTINUATION	$352,593
2024	2023	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	6	11/29/2023	COMPETING CONTINUATION	$0
2024	2022	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	001	5	3/14/2024	NON-COMPETING CONTINUATION	-$352,593
														Subtotal = $529,832

Issue Date FY: 2023 ( Subtotal = $540,645 )
2023	2023	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	001	6	9/15/2023	COMPETING CONTINUATION	$540,645
2023	2022	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	5	9/14/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $540,645

Issue Date FY: 2022 ( Subtotal = $600,717 )
2022	2022	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	5	5/27/2022	NON-COMPETING CONTINUATION	$600,717
														Subtotal = $600,717

Issue Date FY: 2021 ( Subtotal = $626,468 )
2021	2021	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	001	4	5/19/2021	NON-COMPETING CONTINUATION	$626,468
2021	2020	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	3	10/27/2020	NON-COMPETING CONTINUATION	$0
														Subtotal = $626,468

Issue Date FY: 2020 ( Subtotal = $607,378 )
2020	2020	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	001	3	5/15/2020	NON-COMPETING CONTINUATION	$607,378
2020	2019	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	2	12/5/2019	NON-COMPETING CONTINUATION	$0
														Subtotal = $607,378

Issue Date FY: 2019 ( Subtotal = $603,378 )
2019	2019	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	2	5/16/2019	NON-COMPETING CONTINUATION	$603,378
														Subtotal = $603,378

Issue Date FY: 2018 ( Subtotal = $665,174 )
2018	2018	INSTITUTE FOR SYSTEMS BIOLOGY	401 TERRY AVE N	SEATTLE	WA	98109	KING	USA	Human Genome Research	000	1	8/15/2018	NEW	$665,174
														Subtotal = $665,174

Grand Total All Awards = $4,703,424

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Dfam: sustainable growth, curation support, and improved quality for mobile element annotation

Award Number: U24HG010136

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

PERIOD OF PERFORMANCE START DATE: 08/15/2018

PERIOD OF PERFORMANCE END DATE: 06/30/2028

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