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Tools for the automatic identification and classification of RNA base pairs

H. Yang
2003 Nucleic Acids Research  
Three programs have been developed to aid in the classification and visualization of RNA structure.  ...  A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and  ...  ACKNOWLEDGEMENTS We would like to thank Dr Xiang-Jun Lu and Dr Zukang Feng for helpful discussions.  ... 
doi:10.1093/nar/gkg529 pmid:12824344 pmcid:PMC168936 fatcat:7lggespahjed7gkylogge4s4l4

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

Mariusz Popenda, Marek Błażewicz, Marta Szachniuk, Ryszard W. Adamiak
2007 Nucleic Acids Research  
The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures.  ...  about base pairs.  ...  ACKNOWLEDGEMENTS This work was supported by the Foundation for Polish Science (SP 01/04) and the Ministry of Education and Science (3T09A014 29) grants to R.W.A.  ... 
doi:10.1093/nar/gkm786 pmid:17921499 pmcid:PMC2238875 fatcat:bi72c7jm35barle6wwkeud2xym

RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

Maciej Antczak, Tomasz Zok, Mariusz Popenda, Piotr Lukasiak, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk
2014 Nucleic Acids Research  
of RNA base pairs.  ...  In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification  ...  RNAView (13) , MC-Annotate (14) , 3DNA and 3DNA/DSSR (15, 16) are the most popular programs for identification and classification of RNA canonical and noncanonical base pairs (see Supplementary Table  ... 
doi:10.1093/nar/gku330 pmid:24771339 pmcid:PMC4086112 fatcat:wzhxoyals5bdnlbwak4v25bawy

ReadXplorer—visualization and analysis of mapped sequences

Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann
2014 Bioinformatics  
A unique specialty of ReadXplorer is the quality classification of the read mappings.  ...  Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data.  ...  providing the TSS list for evaluation and the research group of Burkhard T€ ummler at the MH Hanover for valuable feedback on the usability of our software.  ... 
doi:10.1093/bioinformatics/btu205 pmid:24790157 pmcid:PMC4217279 fatcat:i6o7gvzc7zbmvn4cg3nbnwlvke

RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data

Qian Zhou, Xiaoquan Su, Gongchao Jing, Songlin Chen, Kang Ning
2018 BMC Genomics  
It has several features that are not available yet in other QC tools for RNA-Seq data, such as RNA sequence trimming, automatic rRNA detection and automatic contaminating species identification.  ...  This package was developed based on our previously reported tool for general QC of next-generation sequencing (NGS) data called QC-Chain, with extensions specifically designed for RNA-Seq data.  ...  Based on the assignment of the classification terms, the taxonomical components of the RNA-Seq data were produced, which indicated whether there was contaminating species, and if so, what these species  ... 
doi:10.1186/s12864-018-4503-6 pmid:29444661 pmcid:PMC5813327 fatcat:o3yatxqhszefraus3uc3an5hjy

Fast and accurate microRNA search using CNN

Xubo Tang, Yanni Sun
2019 BMC Bioinformatics  
Automatic feature learning in CNN can lead to better classification accuracy and sensitivity for miRNA classification and annotation.  ...  The comparison with the state-of-the-art ncRNA classification tools such as Infernal shows that our method can achieve comparable sensitivity and accuracy while being significantly faster.  ...  For a sequence s, the size of the matrix is |s| × |s|. P i,j is the predicted base pairing probability between the ith and jth base in s if the probability p is above a given threshold T.  ... 
doi:10.1186/s12859-019-3279-2 pmid:31881831 pmcid:PMC6933638 fatcat:pbktr6xa4rhwvemkloky5kxx5u

ORFhunteR: an accurate approach for the automatic identification and annotation of open reading frames in human mRNA molecules [article]

Vasily V Grinev, Mikalai M Yatskou, Victor V Skakun, Maryna K Chepeleva, Petr V Nazarov
2021 bioRxiv   pre-print
The developed methods and pre-trained classification model were implemented in a powerful ORFhunteR computational tool that performs an automatic identification of true ORFs among large set of human mRNA  ...  Results: We developed a computational approach, corresponding machine learning model and a package, dedicated to automatic identification of the ORFs in large sets of human mRNA molecules.  ...  The proposed computational approach for the automatic identification of the true ORFs integrates algorithms for vectorization (Zakirava, et al., 2019) and random forest-based classification (Breiman  ... 
doi:10.1101/2021.02.05.429963 fatcat:ifyv4nqczjcx3onebsneffgt6q

New in silico approach to assessing RNA secondary structures with non-canonical base pairs

Agnieszka Rybarczyk, Natalia Szostak, Maciej Antczak, Tomasz Zok, Mariusz Popenda, Ryszard Adamiak, Jacek Blazewicz, Marta Szachniuk
2015 BMC Bioinformatics  
and RNApdbee for base-pair annotation.  ...  Conclusions: The presented methodology ties together existing applications for RNA 3D structure prediction and base-pair annotation.  ...  Thus, an identification of various types of base pairs must be done by the user in additional sequence-based analysis.  ... 
doi:10.1186/s12859-015-0718-6 pmid:26329823 pmcid:PMC4557229 fatcat:f67fkjbajjg6lmd6paxmy3mgjy

Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups

Andreas J. Stroehlein, Neil D. Young, Robin B. Gasser
2018 Scientific Reports  
Accurate annotation requires a reliable and, preferably, automated procedure for the identification of genes and classification of inferred protein sequences.  ...  Nevertheless, algorithms allow automatic searches and comparisons of biological sequences, as well as the identification of conserved patterns and/or domains 8 .  ...  Support from the Melbourne Bioinformatics Platform and WormBase (www.wormbase.org), the Australian Academy of Science, the Australian-American Fulbright Commission, Australia, Alexander von Humboldt Foundation  ... 
doi:10.1038/s41598-018-25020-8 pmid:29717207 pmcid:PMC5931623 fatcat:bmqr4zj6kvfgto3j2v7uprks3q

jViz.RNA 4.0—Visualizing pseudoknots and RNA editing employing compressed tree graphs

Boris Shabash, Kay C. Wiese, Alexander P. Gultiaev
2019 PLoS ONE  
In this work, we present our novel pseudoknot classification and implementation of pseudoknot visualization in the context of the new RNA graph model.  ...  Users are now able to visualize pseudoknotted RNA, manipulate the resulting automatic layouts to suit their individual needs, and change both positioning and connectivity of the RNA molecules examined.  ...  The visualizations produced by VARNA [29] , Forna [31] , and RiboSketch [30] allow for the identification of RNA structural elements as well, however they do not induce a quick identification of the  ... 
doi:10.1371/journal.pone.0210281 pmid:31059508 pmcid:PMC6502502 fatcat:k5k76i2g5jdtvojaen6tkh5ccm

A Review of Computational Methods for Finding Non-Coding RNA Genes

Qaisar Abbas, Syed Raza, Azizuddin Biyabani, Muhammad Jaffar
2016 Genes  
Lastly, we review the limitations of ncRNA gene-finding CI methods with a point-of-view towards the development of new computational tools.  ...  We differentiate from the existing bodies of research and discuss concisely the technical merits of various techniques.  ...  Qaisar Abbas, Syed Mansoor Raza, Azizuddin Ahmed Biyabani, and Arfan Jafar analyzed the problem and wrote the paper. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes7120113 pmid:27918472 pmcid:PMC5192489 fatcat:7tyokbnw6jhd7gqgvz2hkhw6di

FRASS: the web-server for RNA structural comparison

Svetlana Kirillova, Silvio CE Tosatto, Oliviero Carugo
2010 BMC Bioinformatics  
Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.  ...  The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison.  ...  Acknowledgements Funding support from the BIN-III programme of the Austrian GEN-AU is gratefully acknowledged as well as the king hospitality at the Vienna University by Prof. Kristina Djinovic.  ... 
doi:10.1186/1471-2105-11-327 pmid:20553602 pmcid:PMC2902451 fatcat:nvw42ektpnbgloru2rwv4uwnw4

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Mariusz Popenda, Marta Szachniuk, Marek Blazewicz, Szymon Wasik, Edmund K Burke, Jacek Blazewicz, Ryszard W Adamiak
2010 BMC Bioinformatics  
One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures.  ...  This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0.  ...  Acknowledgements The authors thank the following undergraduates from Poznan University of Technology: Natalia Bartol, Karol Bonenberg, Gabriel Kaczmarek, Adam Starikiewicz, Jakub Staszak and Tomasz Zok  ... 
doi:10.1186/1471-2105-11-231 pmid:20459631 pmcid:PMC2873543 fatcat:2e6x7brd5vc7zcgso6trerwbui

HBexplore—a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules

Klaus Lindauer, Cezar Bendic, Jürgen Sühnel
1996 Bioinformatics  
classification of each H-bond according to the participation of backbone, sidechain or base, ligand and water parts of nucleic acids or proteins, identification of Watson-Crick nucleotide pairs and of  ...  These tools include the calculation of mean values and distributions of geometrical hydrogen bond parameters for parts of a single structure, for complete single structures and for structure sets, the  ...  McDonald for making available his excellent program HBPLUS.  ... 
doi:10.1093/bioinformatics/12.4.281 fatcat:qmeme4t63rhqzbj5acfoi5ky4q

BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches

2019 Nucleic Acids Research  
To the best of our knowledge, the BioSeq-Analysis2.0 is the first tool for generating predictors for biological sequence analysis tasks at residue level.  ...  However, the BioSeq-Analysis can be only applied to the sequence-level analysis tasks, preventing its applications to the residue-level analysis tasks, and an intelligent tool that is able to automatically  ...  ACKNOWLEDGEMENTS We are very much indebted to the three anonymous reviewers, whose constructive comments are very helpful for strengthening the presentation of this paper. FUNDING  ... 
doi:10.1093/nar/gkz740 pmid:31504851 pmcid:PMC6847461 fatcat:kziprf5fxjcc5g5irmxrk5hyse
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