Thursday, October 30, 2025 10/30/2025

Machine learning approaches for improved accuracy and speed in sequence annotation

Award Number: R01GM132600
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/20/2019
PERIOD OF PERFORMANCE END DATE: 07/31/2024

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Machine learning approaches for improved accuracy and speed in sequence annotation - Summary/Abstract Alignment of biological sequences is a key step in understanding their evolution, function, and patterns of activity. Here, we describe Machine Learning approaches to improve both accuracy and speed of highly- sensitive sequence alignment. To improve accuracy, we develop methods to reduce erroneous annotation caused by (1) the existence of low complexity and repetitive sequence and (2) the overextension of alignments of true homologs into unrelated sequence. We describe approaches based on both hidden Markov models and Artificial Neural Networks to dramatically reduce these sorts of sequence annotation error. We also address the issue of annotation speed, with development of a custom Deep Learning architecture designed to very quickly filter away large portions of candidate sequence comparisons prior to the relatively-slow sequence-alignment step. The results of these efforts will be incorporated into forks of the open source sequence alignment tools HMMER, MMSeqs, and (where appropriate) BLAST; we will also work with community developers of annotation pipelines, such as RepeatMasker and IMG/M, to incorporate these approaches. The development and incorporation into these widely used bioinformatics tools will lead to widespread impact on sequence annotation efforts.


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: 2023 ( Subtotal = $16,516 )
2023	2022	UNIVERSITY OF ARIZONA	845 N PARK AVE RM 538	TUCSON	AZ	85721	PIMA	USA	Biomedical Research and Research Training	001	5	8/21/2023	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$252,065
2023	2022	UNIVERSITY OF ARIZONA	845 N PARK AVE RM 538	TUCSON	AZ	85721	PIMA	USA	Biomedical Research and Research Training	005	5	9/21/2023	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$233,665
2023	2022	UNIVERSITY OF MONTANA	32 CAMPUS DR	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	000	4	8/18/2023	NON-COMPETING CONTINUATION	-$235,549
2023	2022	UNIVERSITY OF MONTANA	32 CAMPUS DR	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	004	4	9/21/2023	NON-COMPETING CONTINUATION	-$51,699
2023	2021	UNIVERSITY OF MONTANA	32 CAMPUS DR	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	002	3	9/21/2023	NON-COMPETING CONTINUATION	-$102,680
2023	2021	UNIVERSITY OF MONTANA	32 CAMPUS DR	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	003	3	9/21/2023	SUPPLEMENT FOR EXPANSION	-$79,286
														Subtotal = $16,516

Issue Date FY: 2022 ( Subtotal = $287,248 )
2022	2022	UNIVERSITY OF MONTANA	32 CAMPUS DR MAIN HALL	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	000	4	7/29/2022	NON-COMPETING CONTINUATION	$287,248
														Subtotal = $287,248

Issue Date FY: 2021 ( Subtotal = $509,283 )
2021	2021	UNIVERSITY OF MONTANA	32 CAMPUS DR MAIN HALL	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	001	3	9/16/2021	SUPPLEMENT FOR EXPANSION	$221,904
2021	2021	UNIVERSITY OF MONTANA	32 CAMPUS DR MAIN HALL	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	000	3	8/9/2021	NON-COMPETING CONTINUATION	$287,379
														Subtotal = $509,283

Issue Date FY: 2020 ( Subtotal = $287,504 )
2020	2020	UNIVERSITY OF MONTANA	32 CAMPUS DR MAIN HALL	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	000	2	8/6/2020	NON-COMPETING CONTINUATION	$287,504
														Subtotal = $287,504

Issue Date FY: 2019 ( Subtotal = $286,435 )
2019	2019	UNIVERSITY OF MONTANA	32 CAMPUS DR MAIN HALL	MISSOULA	MT	59812	MISSOULA	USA	Biomedical Research and Research Training	000	1	9/19/2019	NEW	$286,435
														Subtotal = $286,435

Grand Total All Awards = $1,386,986

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Machine learning approaches for improved accuracy and speed in sequence annotation

Award Number: R01GM132600

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/20/2019

PERIOD OF PERFORMANCE END DATE: 07/31/2024

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