Evidence map›Paper›PMID 39764445›Full record

ArticleFrontiers in microbiology2024

dna2bit: high performance genomic distance estimation software for microbial genome analysis.

Juzeng Li, Yuxin Tian, Yi Wang, Li Jin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Juzeng Li *Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
Yuxin Tian *Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
Yi WangMinistry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
Li JinMinistry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

dna2bit is an ultra-fast software specifically engineered for microbial genome analysis, particularly adept at calculating genome distances within metagenome and single amplified genome datasets. Distinguished from existing software such as Mash and Dashing, dna2bit employs feature hashing technique and Hamming distance to achieve enhanced speed and memory utilization, without sacrifice in the accuracy of average nucleotide identity calculations. dna2bit has promising applications in various domains such as average nucleotide identity approximation, metagenomic sequence clustering, and homology querying. dna2bit significantly boosts computational efficiency in handling large datasets including single amplified genomes, thereby facilitating a better understanding of the population heterogeneity and comparative genomics of microorganisms. dna2bit is available at https://github.com/lijuzeng/dna2bit.

Indexed as

average nucleotide identitygenome distanceHamming distancemetagenomic clusteringsingle amplified genomes

Identifiers

PMID39764445
PMCPMC11701053

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.