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An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models

BMC Bioinformatics(2024)10.1186/s12859-024-05879-3Source: DataRank Database

An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models is a research paper published in BMC Bioinformatics (2024). On theSindex it has a DataRank of 0.467. It has been cited 7 times, with 6 citing works in its 1-hop citation network.

N/A

0.467DataRank · unranked

Scored on demand from live citation data

Open Access7 citations · 6 citing works in its network

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›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (4 grants)Impact (FWCI 1.09)OA: goldTopics (51)IDs (PubMed, PMC, OpenAlex)Annotations (1)

FAIR Checklist

Context only (not used in score)

Findable (1/2)

Has DOI

Accessible (1/2)

Open Access

Interoperable (0/2)

Reusable (0/3)

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DataRank Breakdown

Base Score 67%Citation Network 33%

Base Score Contribution

0.312

From this paper's citation signal

Citation Network Contribution

0.155

From 2 citing papers with measurable signal

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Top 5 citers driving the network score

Ranked by each citer's contribution to N(p) — log1p(C_q) divided by its reference count — out of 6 citers.

GPU-accelerated homology search with MMseqs2
Nature Methods202545 citations37 referencesContributes 0.103
GPU-accelerated homology search with MMseqs2
bioRxiv (Cold Spring Harbor Laboratory)202419 citations38 referencesContributes 0.079
Method for designing specialized computing systems on the basis of hardware and software cooptimization
Russian Technological Journal20250 citations13 referencesContributes 0.000
Exploration of AI-Driven Genomic and Proteomic Sequence Analysis Landscape
20250 citations458 referencesContributes 0.000
Accurate identification of cytochrome P450 proteins using multimodal integration of protein language models
International Journal of Biological Macromolecules20260 citations39 referencesContributes 0.000

Authors (2)

Travis J. Wheeler ORCID,Tim Anderson

Live enrichment

PubMed:39075359 PMC:PMC11285124 OpenAlex:https://openalex.org/W4401084423

National Institute of General Medical Sciences

Grant: P20GM103546

U.S. Department of Energy

Grant: DE-SC0021216

National Institutes of Health

Grant: 7R01GM132600-05

Machine learning approaches for improved accuracy and speed in sequence annotation

National Institutes of Health

Grant: 5P20GM103546-09

Biomolecular Structure and Dynamics

FWCI

1.09

Citation Percentile

0.8%

Citation Trend

2024

2025

2026

goldLicense: cc-by

journalhttps://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05879-3

publisherhttps://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05879-3

publisherhttps://link.springer.com/content/pdf/10.1186/s12859-024-05879-3.pdf

publisherhttps://link.springer.com/article/10.1186/s12859-024-05879-3/fulltext.html

journalhttps://doi.org/10.1186/s12859-024-05879-3

Fields of Study

Genomics and Phylogenetic StudiesMachine Learning in BioinformaticsGenomics and Rare DiseasesBiologyComputer ScienceMedicine0301 basic medicine0206 medical engineering02 engineering and technology03 medical and health sciencesMarkov ChainsSequence AlignmentComputational BiologySequence HomologyAlgorithmsSoftware

MeSH Terms

AlgorithmsMarkov ChainsSoftwareSequence AlignmentSequence HomologyComputational Biology

Keywords

Field-programmable gate arrayComputer scienceHardware accelerationHidden Markov modelHomology (biology)Markov chainSequence (biology)Computational biologyDNA microarraySequence motifEmbedded systemComputer hardwareBiologyArtificial intelligenceGeneticsMachine learningGeneSequence alignmentFpgaProfile Hidden Markov ModelQH301-705.5ResearchComputer applications to medicine. Medical informaticsR858-859.7Sequence HomologyMarkov ChainsBiology (General)AlgorithmsSoftware