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Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection [chapter]

Yvan Saeys, Yves Van de Peer
2007 Lecture Notes in Computer Science  
To this end, we combine different, complementary sequence features together with a feature selection strategy.  ...  In this paper, we present new methods that specifically aim at a better prediction of coding potential in short sequences.  ...  These results justify that a combined approach for coding potential prediction provides a better model to detect coding potential in short (and even longer) sequences.  ... 
doi:10.1007/978-3-540-71037-0_7 fatcat:xdlwscsxpjehjmzaztwl75n6tm

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

Y. Saeys, P. Rouze, Y. Van de Peer
2007 Bioinformatics  
The main conclusions drawn from our analyses are that 1) combining complementary sequence features clearly outperforms current Markov models for coding potential prediction in short sequence fragments,  ...  The methods use complementary sequence features, combined with identification of which features are relevant in discriminating between coding and non-coding sequences.  ...  Therefore, methods that assess the coding potential in short sequences are of major importance in gene prediction and genome annotation.  ... 
doi:10.1093/bioinformatics/btl639 pmid:17204465 fatcat:ztdhexrdgfd4tkjtv3lpjy5tju

Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features

Jie Lv, Hongbo Liu, Zhijun Huang, Jianzhong Su, Hongjuan He, Youcheng Xiu, Yan Zhang, Qiong Wu
2013 Nucleic Acids Research  
In silico prediction of genomic long non-coding RNAs (lncRNAs) is prerequisite to the construction and elucidation of non-coding regulatory network.  ...  lncRNA and coding genes, which would guide further lncRNA identifications and characterizations.  ...  ACKNOWLEDGEMENTS The authors thank two anonymous referees for their important suggestions. The authors also thank National Natural Science Foundation of China for funding.  ... 
doi:10.1093/nar/gkt818 pmid:24038472 pmcid:PMC3905897 fatcat:q5v5r3izobe3zceyslkzu6zqju

Novel sequencing technologies and bioinformatic tools for deciphering the non-coding genome

Jana Marie Schwarz, Richard Lüpken, Dominik Seelow, Birte Kehr
2021 Medizinische Genetik  
bioinformatic tools for the prediction of effects variants may have in the non-coding part of the genome.  ...  In this review, we provide an overview about how novel sequencing techniques and state-of-the-art algorithms can be used to discover small and structural variants across the whole genome and introduce  ...  Detecting variation through whole genome sequencing Short read sequencing is the most established and widely used technology for studying variation in whole genomes.  ... 
doi:10.1515/medgen-2021-2072 fatcat:dec3cgwpzbhjxn6ult6yrz7vny

Review of Computational Prediction of Competing Endogenous RNA

Sherin K, Achuthsankar S. Nair
2019 Journal of Proteomics & Bioinformatics  
Sudhakaran (Emeritus Professor, Dept. of Computational Biology and Bioinformatics, University of Kerala) for his critical comments in preparing this review article.  ...  Potential binding sequences have the potential binding sites i. e. the complementary sequences corresponding to the seed site of miRNA.  ...  RNA spans from very short RNAs to long non coding RNAs.  ... 
doi:10.4172/0974-276x.1000493 fatcat:el3yzjj36rbfbo3e2aqv4db3fm

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes

G. Solda, I. V. Makunin, O. U. Sezerman, A. Corradin, G. Corti, A. Guffanti
2009 Briefings in Bioinformatics  
Computational methods for ncRNA research require different approaches from the ones normally used in the prediction of protein-coding genes.  ...  for long and short ncRNA identification and annotation. since 1999.  ...  Assessment of the protein-coding potential As long ncRNAs generally lack discernable features to facilitate categorization and functional prediction, the most widely used strategy to annotate a ncRNA is  ... 
doi:10.1093/bib/bbp022 pmid:19383843 fatcat:ham63whbwnfflkuvqjnwqnl6ay

A Novel Position-Specific Encoding Algorithm (SeqPose) of Nucleotide Sequences and Its Application for Detecting Enhancers

Xuechen Mu, Yueying Wang, Meiyu Duan, Shuai Liu, Fei Li, Xiuli Wang, Kai Zhang, Lan Huang, Fengfeng Zhou
2021 International Journal of Molecular Sciences  
Enhancers are short genomic regions exerting tissue-specific regulatory roles, usually for remote coding regions.  ...  Most of the current studies utilized the statistical features of short fixed-length nucleotide sequences.  ...  Acknowledgments: Insightful and constructive comments from the anonymous reviewers are greatly appreciated. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms22063079 pmid:33802922 pmcid:PMC8002641 fatcat:rwjoectswjdelp5azgaa6cbr6i

Repeats Mimic Immunostimulatory Viral Features Across a Vast Evolutionary Landscape [article]

Petr Šulc, Alexander Solovyov, Sajid A Marhon, Siyu Sun, John A LaCava, Omar I. Abdel-Wahab, Nicolas Vabret, Daniel De Carvalho, Rémi Monasson, Simona Cocco, Benjamin D. Greenbaum
2021 bioRxiv   pre-print
We show that for HSATII and intact LINE-1 selective forces maintain CpG motifs, while for a set of SINE and LINE elements the formation of long double-stranded RNA is more prevalent than expected from  ...  Here we propose a theoretical framework that combines recent biological observations with statistical physics and population genetics to quantify the selective forces on virus-like features generated by  ...  between sequences and is easily interpretable as the information theoretic cost of avoiding or enhancing specific features in a sequence.  ... 
doi:10.1101/2021.11.04.467016 fatcat:enyvypah7ng3zlgtx3ozfojjwm

HomoTarget: A new algorithm for prediction of microRNA targets in Homo sapiens

Hamed Ahmadi, Ali Ahmadi, Sadegh Azimzadeh-Jamalkandi, Mahdi Aliyari Shoorehdeli, Ali Salehzadeh-Yazdi, Gholamreza Bidkhori, Ali Masoudi-Nejad
2013 Genomics  
Using the recent release of the mirBase database to find potential targets of miRNAs, this model incorporated twelve structural, thermodynamic and positional features of miRNA:mRNA binding sites to select  ...  Several computational approaches have been proposed for the prediction of miRNA target-genes. Reports reveal a large fraction of under-predicted or falsely predicted target genes.  ...  Amene Javid for proof-reading the article. We appreciate help from Dr. Vinod CSS for providing us some database of miRNA targets and valuable discussion on early stage of this work. Appendix A.  ... 
doi:10.1016/j.ygeno.2012.11.005 pmid:23174671 fatcat:yeh2fhrf7rarfhigswb5kzu524

Next-generation libraries for robust RNA interference-based genome-wide screens

Martin Kampmann, Max A. Horlbeck, Yuwen Chen, Jordan C. Tsai, Michael C. Bassik, Luke A. Gilbert, Jacqueline E. Villalta, S. Chul Kwon, Hyeshik Chang, V. Narry Kim, Jonathan S. Weissman
2015 Proceedings of the National Academy of Sciences of the United States of America  
Here, we systematically optimize several aspects of our shRNA library, including the promoter and microRNA context for shRNA expression, selection of guide strands, and features relevant for postscreen  ...  sample preparation for deep sequencing.  ...  Taking into account additional features did not improve the predictive power of the sequence score, because many of the sequence features are correlated for shRNAs generated by the Hannon laboratory shRNA  ... 
doi:10.1073/pnas.1508821112 pmid:26080438 pmcid:PMC4491794 fatcat:7vzuwwpmv5gorjacyvnx3gixsm

Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli

Sergey A. Evfratov, Ilya A. Osterman, Ekaterina S. Komarova, Alexandra M. Pogorelskaya, Maria P. Rubtsova, Timofei S. Zatsepin, Tatiana A. Semashko, Elena S. Kostryukova, Andrey A. Mironov, Evgeny Burnaev, Ekaterina Krymova, Mikhail S. Gelfand (+4 others)
2016 Nucleic Acids Research  
In addition to known ones, several previously unrecognized features that contribute to the translation enhancement were found, such as low proportion of cytidine residues, multiple SD sequences and AG  ...  We tested efficiency of translation of the CER gene preceded by each of 48 natural 5 -UTR sequences and introduced random and designed mutations into natural and artificially selected 5 -UTRs.  ...  Automatic selection of features influencing translation enhancement We then applied automatic machine learning methods to construct predictive models for translation efficiency and extract features of  ... 
doi:10.1093/nar/gkw1141 pmid:27899632 pmcid:PMC5389652 fatcat:l4sm52i4qnawxh332fdkupp5ci

Enhanced graphic matrix analysis of nucleic acid and protein sequences

J. V. Maizel, R. P. Lenk
1981 Proceedings of the National Academy of Sciences of the United States of America  
analyzes nucleic acid and amino acid sequences for features ofpossible biological interest and reveals the spatial patterns ofsuch features.  ...  Genetics Enhanced graphic matrix analysis of nucleic acid and protein sequences (sequence homology/transposition/secondary structure/immunoglobulin/microcomputer) ABSTRACT The enhanced graphic matrix procedure  ...  We thank Jon Seidman for providing sequences and electron micrographs and encouraging the development of these programs, M. Waterman (Los Alamos Scientific Laboratories) and B. Bush and C.  ... 
doi:10.1073/pnas.78.12.7665 pmid:6801656 pmcid:PMC349330 fatcat:lhkqoau4pnfvdhpkel6vbu4ay4

Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm

Supatcha Lertampaiporn, Chinae Thammarongtham, Chakarida Nukoolkit, Boonserm Kaewkamnerdpong, Marasri Ruengjitchatchawalya
2014 Nucleic Acids Research  
This feature is generated based on a logistic regression function that combines five significant features--structure, sequence, modularity, structural robustness and coding potential--to enable improved  ...  short ncRNA sequences as well as long complex ncRNA sequences.  ...  To address the diversity in ncRNA families, our selected feature subset was composed of various complementary features that could enhance RF performance by capturing most possible aspects of heterogeneity  ... 
doi:10.1093/nar/gku325 pmid:24771344 pmcid:PMC4066759 fatcat:xa3vdwhzmbhelekuzqavdzt2k4

An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants

Ajay Prakash Uniyal, Komal Mansotra, Sudesh Kumar Yadav, Vinay Kumar
2019 3 Biotech  
In fact, the sequence of sgRNA is considered an important parameter to determine the efficiency and specificity of sgRNAs for precise genome editing.  ...  Interestingly, all these selected tools generated different results (sgRNAs) even for the same query.  ...  The authors thank anonymous reviewers and editors for critical reading the manuscript and suggesting substantial improvements. Author contributions VK conceived and designed the present research.  ... 
doi:10.1007/s13205-019-1760-2 pmid:31139538 pmcid:PMC6529479 fatcat:ucrzubq72fgrpd27fre6y5qh5m

Prediction of enhancer-promoter interactions via natural language processing

Wanwen Zeng, Mengmeng Wu, Rui Jiang
2018 BMC Genomics  
Conclusions: EP2vec sheds light on feature extraction for DNA sequences of arbitrary lengths and provides a powerful approach for EPIs identification.  ...  Then, we train a classifier to predict EPIs using the learned representations in supervised way.  ...  Acknowledgments Rui Jiang is a RONG professor at the Institute for Data Science, Tsinghua University. We acknowledge the authors of TargetFinder, who provide us valuable data.  ... 
doi:10.1186/s12864-018-4459-6 pmid:29764360 pmcid:PMC5954283 fatcat:srm6qowqh5c5xmg4gwhyt5ecum
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