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Classification of Precursor MicroRNAs from Different Species Based on K-mer Distance Features

Malik Yousef, Jens Allmer
2021 Algorithms  
We have previously shown that it is possible to distinguish between microRNA precursors of different clades by representing the sequences in a k-mer feature space.  ...  Here, we show that classification performance above 80% (depending on the evolutionary distance) is possible with a combination of distance-based and regular k-mer features.  ...  Availability and Implementation: We performed all analysis using the KNIME platform and have made the analysis workflow available at GitHub: https://github.com/malikyousef/microRNAsbased-on-K-mer-Distance-Features  ... 
doi:10.3390/a14050132 doaj:ef01af41922545cc878e3a182b36b050 fatcat:74ejw4ia7faxfgcduorginrige

Prediction of Mature MicroRNA and Piwi-Interacting RNA without a Genome Reference or Precursors

Mark Menor, Kyungim Baek, Guylaine Poisson
2015 International Journal of Molecular Sciences  
In this study, we propose an approach that relies primarily on the nucleotide composition of the read and does not require reference genomes of related species for prediction.  ...  The discovery of novel microRNA (miRNA) and piwi-interacting RNA (piRNA) is an important task for the understanding of many biological processes.  ...  Acknowledgments This work is supported in part by an NIH grant from the National Institute of General Medical Sciences (P20GM103516).  ... 
doi:10.3390/ijms16011466 pmid:25580537 pmcid:PMC4307313 fatcat:hrildyi4mfba5gquiaqujsvpvi

Ensemble Clustering Classification Applied to Competing SVM and One-Class Classifiers Exemplified by Plant MicroRNAs Data

Malik Yousef, Waleed Khalifa, Loai AbdAllah
2016 Journal of Integrative Bioinformatics  
The comparison was applied to seven different plant microRNA species considering eight feature selection methods.  ...  We have demonstrated that the k-nearest neighbor (kNN) classification can be significantly improved by learning a distance metric from labeled examples.  ...  These simple features, also called words, k-mers, or n-grams, describe a short sequence of nucleotides of length k or n.  ... 
doi:10.1515/jib-2016-304 fatcat:au3kzxssn5hhpojjbrnzsqabrm

PlantMirP2: An Accurate, Fast and Easy-To-Use Program for Plant Pre-miRNA and miRNA Prediction

Dashuai Fan, Yuangen Yao, Ming Yi
2021 Genes  
In our previous studies, we have put firstly forward and further developed a set of knowledge-based energy features to construct two plant pre-miRNA prediction tools (plantMirP and riceMirP).  ...  MicroRNAs (miRNAs) are a kind of short non-coding ribonucleic acid molecules that can regulate gene expression.  ...  PlantMirP is the first plant pre-miRNA tool with knowledge-based energy features calculated from distance-specific k-mer pair potentials.  ... 
doi:10.3390/genes12081280 pmid:34440454 pmcid:PMC8392394 fatcat:w2xgdpwg6zga5bhrl3gogk6mrq

IpiRId: Integrative approach for piRNA prediction using genomic and epigenomic data

Anouar Boucheham, Vivien Sommard, Farida Zehraoui, Adnane Boualem, Mohamed Batouche, Abdelhafid Bendahmane, David Israeli, Fariza Tahi, Bin Liu
2017 PLoS ONE  
A common step in these methods is feature extraction in which many features or k-mers are generated or in some cases extracted from strings based on specific observations.  ...  K-mers are largely applied for sequence analysis, especially in the identification of ncRNAs, where many k-mer-based approaches have been proposed in the last years, as for piRNAs and microRNAs [10, 12  ... 
doi:10.1371/journal.pone.0179787 pmid:28622364 pmcid:PMC5473586 fatcat:up67qocubrhsjellqhocvjrb4u

Characterization and Identification of MicroRNA Core Promoters in Four Model Species

Xuefeng Zhou, Jianhua Ruan, Guandong Wang, Weixiong Zhang
2007 PLoS Computational Biology  
Among these motifs, some are conserved across different species while some are specific to microRNA genes of individual species.  ...  Using this new method, we identify putative core promoters of most known microRNA genes in the four model species. Moreover, we characterize the promoters of microRNA genes in these four species.  ...  This research was supported in part by US National Science Foundation grants ITR/EIA-0113618 and IIS-0535257 and by a grant from Monsanto, all to WZ. Competing interests.  ... 
doi:10.1371/journal.pcbi.0030037 pmid:17352530 pmcid:PMC1817659 fatcat:amw4g3olwvdx3gjxfbbto4tnre

Effective sample selection for classification of pre-miRNAs

K. Han
2011 Genetics and Molecular Research  
Real/ pseudo pre-miRNAs are clustered based on their stem similarity and their distribution in high dimensional sample space, respectively.  ...  To solve the class imbalance problem in the classification of pre-miRNAs with the ab initio method, we developed a novel sample selection method according to the characteristics of pre-miRNAs.  ...  The nucleotides are different at irregular intervals. It is found that there are more same 4-mers in the similar pre-miRNAs from the 3 species.  ... 
doi:10.4238/vol10-1gmr1054 pmid:21476196 fatcat:fh2r4u2ttfeh5hivb37w7wiini

ExtendAlign: a computational algorithm for delivering multiple, local end-to-end alignments [article]

Mariana Flores-Torres, Laura Gómez-Romero, Joshua I. Haase-Hernández, Israel Aguilar-Ordóñez, Hugo Tovar, S. Eréndira Avendaño-Vázquez, C. Fabián Flores-Jasso
2018 bioRxiv   pre-print
We tested the efficacy of ExtendAlign using mature and precursor microRNAs versus unrelated distant genomes because of their relevance in the discovery of novel small RNAs.  ...  Conversely, MSATs that perform global alignments deal better with dissimilar sequences, but at the cost of introducing gaps.  ...  Because new microRNA candidates deposited in miRBase began to accumulate swiftly, a new set of rules for novel microRNA annotation based on structural features has emerged.  ... 
doi:10.1101/475707 fatcat:yxgzhbf7nfhxtfsl2sz6epfoqm

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data [article]

Carol Moraga, Evelyn Sanchez, Mariana Galvao Ferrarini, Rodrigo A Gutierrez, Elena A Vidal, Marie-France Sagot
2020 bioRxiv   pre-print
In the last decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on pre-existing reference  ...  The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animals species.  ...  Such features distinguish BrumiR from the current genome-based methods. Discovering miRNAs in non-model species is one of the limitations of the current methods.  ... 
doi:10.1101/2020.08.07.240689 fatcat:mgmoxdbhfrhxxmokcjptdjscgi

A first Glimpse at the genome of the Baikalian amphipodEulimnogammarus verrucosus

Lorena Rivarola-Duarte, Christian Otto, Frank Jühling, Stephan Schreiber, Daria Bedulina, Lena Jakob, Anton Gurkov, Denis Axenov-Gribanov, Abdullah H. Sahyoun, Magnus Lucassen, Jörg Hackermüller, Steve Hoffmann (+5 others)
2014 Journal of Experimental Zoology Part B: Molecular and Developmental Evolution  
We report here on a survey sequencing of its genome as a first step to establish sequence resources for this species.  ...  Using a seed-based approach we nevertheless assembled short contigs covering 33 pre-microRNAs and the homeodomain-containing exon of nine Hox genes.  ...  Supplemental Material consisting of additional information on methods, tables, and figures is available as a PDF document.  ... 
doi:10.1002/jez.b.22560 pmid:24677529 fatcat:ygmobfwv4zapvh65nclkvgpvtm

Learning from positive examples when the negative class is undetermined- microRNA gene identification

Malik Yousef, Segun Jung, Louise C Showe, Michael K Showe
2008 Algorithms for Molecular Biology  
However, some one-class methods outperform some recently published two-class approaches with different selected features.  ...  We also examine the ability of the one-class and two-class techniques to identify miRNAs in newly sequenced species.  ...  Acknowledgements This project is funded in part under a grant with the Pennsylvania Department of Health (PA DOH Commonwealth Universal Research Enhancement Program), and Tobacco Settlement grants ME01  ... 
doi:10.1186/1748-7188-3-2 pmid:18226233 pmcid:PMC2248178 fatcat:yc35cgpwvrborix3vni2itz4n4

Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements

Ilektra-Chara Giassa, Panagiotis Alexiou
2021 Biology  
Transposable elements (TEs, or mobile genetic elements, MGEs) are ubiquitous genetic elements that make up a substantial proportion of the genome of many species.  ...  In this review, we provide a guided overview of the bioinformatic and machine learning state of the art of fields closely associated with TE regulation and function.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biology10090896 pmid:34571773 pmcid:PMC8465862 fatcat:5a5osyvzfjhc3jogue42lgrtyy

Using a kernel density estimation based classifier to predict species-specific microRNA precursors

Darby Chang, Chih-Ching Wang, Jian-Wei Chen
2008 BMC Bioinformatics  
Results: This study focuses on the classification algorithm for miRNA prediction. We develop a novel ab initio method, miR-KDE, in which most of the features are collected from previous works.  ...  The good performance of miR-KDE encourages more efforts on the classification methodology as well as the feature extraction in miRNA prediction.  ...  This article has been published as part of BMC Bioinformatics Volume 9 Supplement 12, 2008: Asia Pacific Bioinformatics Network (APBioNet) Seventh International Conference on Bioinformatics (InCoB2008)  ... 
doi:10.1186/1471-2105-9-s12-s2 pmid:19091019 pmcid:PMC2638167 fatcat:fnlvz6kk5bcfxhlxrhic4qa34y

An in-silico approach to study the possible interactions of miRNA between human and SARS-CoV2

Abhijit Sarma, Homen Phukan, Neha Halder, Madathiparambil Gopalakrishnan Madanan
2020 Computational biology and chemistry  
Based on the prediction and analysis, we have identified 22 potential miRNAs from five genomes of SARS-CoV2 linked with 12 human miRNAs.  ...  MicroRNAs are the small non-coding RNAs that help in regulating gene profiling.  ...  Funding This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Appendix A.  ... 
doi:10.1016/j.compbiolchem.2020.107352 pmid:32771962 pmcid:PMC7395633 fatcat:ydftduzdezav7hjmpgwredjape

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

Wenyan Nong, Jianquan Cao, Yiqian Li, Zhe Qu, Jin Sun, Thomas Swale, Ho Yin Yip, Pei Yuan Qian, Jian-Wen Qiu, Hoi Shan Kwan, William Bendena, Stephen Tobe (+7 others)
2020 Nature Communications  
Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.  ...  Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected  ...  were analysed based on a k-mer-based statistical approach in the GenomeScope webtool 77 .  ... 
doi:10.1038/s41467-020-16801-9 pmid:32561724 fatcat:hv6btf4cufcnrbvoua3k56vo7i
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