ArticleScientific reports2016
NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 37 citations in OpenAlex.
- The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation.RNA biology · 2025Review
- Small Interfering RNAs as Critical Regulators of Plant Life Process: New Perspectives on Regulating the Transcriptomic Machinery.International journal of molecular sciences · 2025Review
- Genome-Wide Identification and Characterization of miRNAs and Natural Antisense Transcripts Show the Complexity of Gene Regulatory Networks for Secondary Metabolism inInternational journal of molecular sciences · 2024Article
- Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L.Plant molecular biology · 2024Article
- CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within specified regions.Scientific reports · 2023Article
- Biogenesis, Mode of Action and the Interactions of Plant Non-Coding RNAs.International journal of molecular sciences · 2023Review
- Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Review
- CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles.Scientific reports · 2022Article
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- Biogenesis, Trafficking, and Function of Small RNAs in Plants.Frontiers in plant science · 2022Article
- Non-Coding RNAs in Response to Drought Stress.International journal of molecular sciences · 2021Review
- Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza.Scientific reports · 2021Article
- The RNA degradome: a precious resource for deciphering RNA processing and regulation codes in plants.RNA biology · 2020Article
- NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs.Nucleic acids research · 2020Article
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- Review
- OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes.Nucleic acids research · 2018Article
- Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers.International journal of molecular sciences · 2018Review
- Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs.Rice (New York, N.Y.) · 2017Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip.
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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.