ArticlePloS one2016
DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Regulatory landscape of widespread stop codon readthrough inbioRxiv : the preprint server for biology · 2026Article
- Organism-Specific Sequence Motifs Link Ribosomal RNAs to Brain Disorders.Molecular biology and evolution · 2025Article
- Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression.PLoS genetics · 2025Article
- Scalable Approach to Evaluate Plant microRNA Trimming and Tailing from Small RNA-Seq Data.Methods in molecular biology (Clifton, N.J.) · 2025Article
- FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing.PLoS computational biology · 2024Article
- PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences.Bioinformatics (Oxford, England) · 2023Article
- The miRNA-mRNA Regulatory Modules ofInternational journal of molecular sciences · 2023Article
- Multiomics of Tissue Extracellular Vesicles Identifies Unique Modulators of Atherosclerosis and Calcific Aortic Valve Stenosis.Circulation · 2023Article
- Review
- Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar.International journal of molecular sciences · 2022Article
- DIANA-miTED: a microRNA tissue expression database.Nucleic acids research · 2022Article
- Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem ofInternational journal of molecular sciences · 2021Article
- Article
- Date palm virus A: first plant virus found in date palm trees.Virus genes · 2020Article
- High-Throughput Identification of Adapters in Single-Read Sequencing Data.Biomolecules · 2020Article
- An Online Database for Exploring Over 2,000 Arabidopsis Small RNA Libraries.Plant physiology · 2020Article
- Are Antisense Proteins in Prokaryotes Functional?Frontiers in molecular biosciences · 2020Article
- A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding GeneFrontiers in microbiology · 2020Article
- Accurate Adapter Information Is Crucial for Reproducibility and Reusability in Small RNA Seq Studies.Non-coding RNA · 2019Article
- Visualization of the small RNA transcriptome using seqclusterViz.F1000Research · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
With the rapid accumulation of publicly available small RNA sequencing datasets, third-party meta-analysis across many datasets is becoming increasingly powerful. Although removing the 3´ adapter is an essential step for small RNA sequencing analysis, the adapter sequence information is not always available in the metadata. The information can be also erroneous even when it is available. In this study, we developed DNApi, a lightweight Python software package that predicts the 3´ adapter sequence de novo and provides the user with cleansed small RNA sequences ready for down stream analysis. Tested on 539 publicly available small RNA libraries accompanied with 3´ adapter sequences in their metadata, DNApi shows near-perfect accuracy (98.5%) with fast runtime (~2.85 seconds per library) and efficient memory usage (~43 MB on average). In addition to 3´ adapter prediction, it is also important to classify whether the input small RNA libraries were already processed, i.e. the 3´ adapters were removed. DNApi perfectly judged that given another batch of datasets, 192 publicly available processed libraries were "ready-to-map" small RNA sequence. DNApi is compatible with Python 2 and 3, and is available at https://github.com/jnktsj/DNApi. The 731 small RNA libraries used for DNApi evaluation were from human tissues and were carefully and manually collected. This study also provides readers with the curated datasets that can be integrated into their studies.
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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.