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RNA-CODE: A Noncoding RNA Classification Tool for Short Reads in NGS Data Lacking Reference Genomes

Cheng Yuan, Yanni Sun, Ali Torkamani
2013 PLoS ONE  
The experimental results of applying RNA-CODE to RNA-seq of Arabidopsis and a metagenomic data set sampled from human guts demonstrate that RNA-CODE competes favorably in both sensitivity and specificity  ...  The classification results can be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively.  ...  NCRNA classification in RNA-seq data To demonstrate the utility of RNA-CODE on detecting reads sequenced from various ncRNA genes, we conducted the second experiment on real RNA-seq data.  ... 
doi:10.1371/journal.pone.0077596 pmid:24204885 pmcid:PMC3808423 fatcat:lprc3bsmdnhinbmnyeogrto3gu

baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data [article]

Alina Ozuna, Doriano Liberto, Rosanna M Joyce, Kristine Bourke Arnvig, Irene Nobeli
2019 bioRxiv   pre-print
Here, we present baerhunter, a method implemented in R, that automates the discovery of expressed non-coding RNAs and UTRs from RNA-seq reads mapped to a reference genome.  ...  Standard bioinformatics pipelines for the analysis of bacterial transcriptomic data commonly ignore non-coding but functional elements e.g. small RNAs, long antisense RNAs or untranslated regions (UTRs  ...  Peña-Castillo,L. et al. (2015) Detection of bacterial small transcripts from rna-seq data: a comparative assessment. In, Biocomputing 2016. WORLD SCIENTIFIC, pp. 456-467.  ... 
doi:10.1101/612937 fatcat:w53pdq2rr5gvhljy37fqe3wywu

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

M. S. Campbell, M. Law, C. Holt, J. C. Stein, G. D. Moghe, D. E. Hufnagel, J. Lei, R. Achawanantakun, D. Jiao, C. J. Lawrence, D. Ware, S.-H. Shiu (+4 others)
2013 Plant Physiology  
RNAs absent from The Arabidopsis Informatics Resource 10 build.  ...  New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification.  ...  Craig Venter Institute for helpful discussion and feedback as well as Suzie Lewis at the University of California, Berkeley, and the rest of the WebApollo team for their efforts to ensure WebApollo compatibility  ... 
doi:10.1104/pp.113.230144 pmid:24306534 pmcid:PMC3912085 fatcat:66akszwoobf33mnj2nfa4p2jpu

Limitations of alignment-free tools in total RNA-seq quantification

Douglas C. Wu, Jun Yao, Kevin S. Ho, Alan M. Lambowitz, Claus O. Wilke
2018 BMC Genomics  
Result: We comprehensively tested and compared four RNA-seq pipelines for accuracy of gene quantification and fold-change estimation.  ...  We used a novel total RNA benchmarking dataset in which small non-coding RNAs are highly represented along with other long RNAs.  ...  Raw RNA-seq dataset can be accessed through NCBI Sequence Read Archive, accession number SRP066009.  ... 
doi:10.1186/s12864-018-4869-5 pmid:29969991 pmcid:PMC6042521 fatcat:k5bjud7pz5dybh7ntsiwn2ewfq

Integrating Epigenomics into the Understanding of Biomedical Insight

Yixing Han, Ximiao He
2016 Bioinformatics and Biology Insights  
In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources  ...  Bioinformatics is expected to make a remarkable contribution for this purpose, especially in processing and interpreting the large-scale NGS datasets.  ...  Small RNA-seq is the popularly used approach for small ncRNA identification; the library construction has a large overlap with the RNA-seq with ribosome RNA elimination, cDNA synthesis, 3′-A addition,  ... 
doi:10.4137/bbi.s38427 pmid:27980397 pmcid:PMC5138066 fatcat:ne6mu3bdhzhzno5hqjvgmxp3nu

GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering

Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Björn Grüning, Rolf Backofen
2019 GigaScience  
We suggest the presence and the sparseness of phylogenetically conserved local structures for a collection of long non-coding RNAs.  ...  Here we present GraphClust2, a comprehensive approach for scalable clustering of RNAs based on sequence and structural similarities.  ...  Acknowledgments We thank Freiburg Galaxy team for their support. We thank Sean Eddy for the helpful comments and discussions. We also thank Sita J.  ... 
doi:10.1093/gigascience/giz150 pmid:31808801 pmcid:PMC6897289 fatcat:d2lexbowt5glhgycldteocgo74

GraphClust: alignment-free structural clustering of local RNA secondary structures

Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen
2012 Computer applications in the biosciences : CABIOS  
A selection of applications aiming at the detection of novel structural ncRNAs are presented.  ...  Motivation: Clustering according to sequence-structure similarity has now become a generally accepted scheme for ncRNA annotation.  ...  unlikely in practical application scenarios, where one often has either a partial transcript (e.g. from RNA-seq data), or just transcripts with wrong boundaries.  ... 
doi:10.1093/bioinformatics/bts224 pmid:22689765 pmcid:PMC3371856 fatcat:o2zyufbcsbdl7labf3jkvfq3jm

Limitation of alignment-free tools in total RNA-seq quantification [article]

Douglas C Wu, Jun Yao, Kevin S Ho, Alan M Lambowitz, Claus O Wilke
2018 bioRxiv   pre-print
Result: We comprehensively tested and compared four RNA-seq pipelines on the accuracies of gene quantification and fold-change estimation on a novel total RNA benchmarking dataset, in which small non-coding  ...  The four RNA-seq pipelines were of two commonly-used alignment-free pipelines and two variants of alignment-based pipelines.  ...  Wu (The Scripps Research Institute) for critical reading of the manuscript, and Ben R. Jack and Dr. Adam J. Hockenberry from the Wilke lab for fruitful discussions and useful insights.  ... 
doi:10.1101/246967 fatcat:ahfeesfuynft7o3nklzkz4efsi

Structure-based whole-genome realignment reveals many novel noncoding RNAs

S. Will, M. Yu, B. Berger
2013 Genome Research  
REAPR's advancement of de novo structural characterization of ncRNAs complements the identification of transcripts from rapidly accumulating RNA-seq data.  ...  Moreover, modENCODE RNA-seq experiments confirm a substantial number of its predictions as transcripts.  ...  Acknowledgments We thank Michael Baym for early discussions on improving wholegenome alignments.  ... 
doi:10.1101/gr.137091.111 pmid:23296921 pmcid:PMC3668356 fatcat:45xdwaivbng4hfdvo4pc4r5rhu

Evaluation of methodologies for microRNA biomarker detection by next generation sequencing

Anna M L Coenen-Stass, Iddo Magen, Tony Brooks, Iddo Z Ben-Dov, Linda Greensmith, Eran Hornstein, Pietro Fratta
2018 RNA Biology  
Here, we have tested in parallel four commercially available small RNA sequencing kits against a cohort of samples comprised of human plasma, human serum, murine brain tissue and a reference library containing  ...  In recent years, microRNAs (miRNAs) in tissues and biofluids have emerged as a new class of promising biomarkers for numerous diseases.  ...  We thank UCL Genomics for their support with the sequencing services. Disclosure statement No potential conflict of interest was reported by the authors.  ... 
doi:10.1080/15476286.2018.1514236 pmid:30223713 pmcid:PMC6161688 fatcat:zrhwkiqtcjelbi3azhjcu3lw4e

Disease-Associated Circular RNAs: From Biology to Computational Identification

Min Tang, Ling Kui, Guanyi Lu, Wenqiang Chen
2020 BioMed Research International  
Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA.  ...  To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications.  ...  This work was supported by a grant from Jiangsu University (19JDG039).  ... 
doi:10.1155/2020/6798590 pmid:32908906 pmcid:PMC7450300 fatcat:ggwwamht4ng4zgtqdqs3shjvk4

Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs [chapter]

Sebastian Will, Michael Yu, Bonnie Berger
2012 Lecture Notes in Computer Science  
Acknowledgments We thank Michael Baym for early discussions on improving wholegenome alignments.  ...  RNA-seq transcriptome data from the modEncode project confirm many of REAPR's predictions in D. melanogaster as transcripts during embryo development.  ...  This site also includes predictions and RNA-seq expression analysis. Figure 1 . 1 The whole-genome REAPR (RE-Alignment for Prediction of structural ncRNAs) pipeline. Figure 2 . 2 Figure 2.  ... 
doi:10.1007/978-3-642-29627-7_35 fatcat:3louvmkzlvfulhj36mch7t4v3i

Defining the functional significance of intergenic transcribed regions [article]

John P. Lloyd, Zing T.-Y. Tsai, Rosalie P. Sowers, Nicholas L. Panchy, Shin-Han Shiu
2017 bioRxiv   pre-print
Next, by applying the models genome-wide, we found that 4,427 ITRs (38%) and 796 annotated ncRNAs (44%) had features significantly similar to benchmark protein-coding or RNA genes and thus were likely  ...  The predictive framework established here provides not only a comprehensive look at how functional, genic sequences are distinct from likely nonfunctional ones, but also a new way to differentiate novel  ...  ACKNOWLEDGEMENTS 648 The authors wish to thank Christina Azodi, Ming-Jung Liu, Gaurav Moghe, Bethany Moore, and 649 Sahra Uygun and for providing processed data and discussion.  ... 
doi:10.1101/127282 fatcat:ylcw35wcl5euzm3di5rbl3z2y4

NAPP: the Nucleic Acid Phylogenetic Profile Database

Alban Ott, Anouar Idali, Antonin Marchais, Daniel Gautheret
2011 Nucleic Acids Research  
In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements  ...  RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software.  ...  The benchmark used a test set of 776 sRNAs from 10 bacterial species, including 132 RNAs from RFAM and the others from RNA-seq and tiling array experiments.  ... 
doi:10.1093/nar/gkr807 pmid:21984475 pmcid:PMC3245103 fatcat:xmo2zoqgcbc35gbshb5cdfuvsa

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies

Maggie C. Y. Lau, Rachel L. Harris, Youmi Oh, Min Joo Yi, Aida Behmard, Tullis C. Onstott
2018 Frontiers in Microbiology  
De novo assembly of RNA-Sequencing (RNA-Seq) data can reveal a more detailed description of the metabolic interactions amongst the active microbial communities.  ...  In this study, we compared 15 de novo metatranscriptomic assemblies for a fracture fluid sample collected from a borehole located at 1.34 km below land surface in a South African gold mine.  ...  Pipelines exist to facilitate such (meta)genomic and (meta)transcriptomic data integration by aligning RNA-Seq reads to genomic templates, for example, IMP (Narayanasamy et al., 2016) and ATLAS (White  ... 
doi:10.3389/fmicb.2018.01235 pmid:29973918 pmcid:PMC6019464 fatcat:f33guinkgvfpbgwtuxhaxvcx5u
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