ArticleFrontiers in microbiology2019
DMSC: A Dynamic Multi-Seeds Method for Clustering 16S rRNA Sequences Into OTUs.
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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.
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.
Who cites it
5 citing papers in PubMed, 18 citations in OpenAlex.
- pathMap: a path-based mapping tool for long noisy reads with high sensitivity.Briefings in bioinformatics · 2024Article
- Article
- Article
- Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences.Frontiers in microbiology · 2021Article
- smsMap: mapping single molecule sequencing reads by locating the alignment starting positions.BMC bioinformatics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS)-based 16S rRNA sequencing by jointly using the PCR amplification and NGS technology is a cost-effective technique, which has been successfully used to study the phylogeny and taxonomy of samples from complex microbiomes or environments. Clustering 16S rRNA sequences into operational taxonomic units (OTUs) is often the first step for many downstream analyses. Heuristic clustering is one of the most widely employed approaches for generating OTUs. However, most heuristic OTUs clustering methods just select one single seed sequence to represent each cluster, resulting in their outcomes suffer from either overestimation of OTUs number or sensitivity to sequencing errors. In this paper, we present a novel dynamic multi-seeds clustering method (namely DMSC) to pick OTUs. DMSC first heuristically generates clusters according to the distance threshold. When the size of a cluster reaches the pre-defined minimum size, then DMSC selects the multi-core sequences (MCS) as the seeds that are defined as the
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.