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BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles

Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen
2014 Computer applications in the biosciences : CABIOS  
A different type of information that does not suffer from these issues and that can be used for the detection of RNA classes, is the pattern of processing and its traces in small RNA-seq reads data.  ...  Non-coding RNAs (ncRNAs) play a vital role in many cellular processes such as RNA splicing, translation, gene regulation. However the vast majority of ncRNAs still have no functional annotation.  ...  in small RNA-seq reads data (Findeiss et al., 2011) .  ... 
doi:10.1093/bioinformatics/btu270 pmid:24931994 pmcid:PMC4058930 fatcat:u665rdwwzvazxlwsmkrgqx7rqi

Emerging applications of read profiles towards the functional annotation of the genome

Sachin Pundhir, Panayiota Poirazi, Jan Gorodkin
2015 Frontiers in Genetics  
, Ministry of Education, Greece and the European Regional Development Fund (Sectoral Operational Programme: Competitiveness and Entrepreneurship, NSRF 2007-2013)/European Commission.  ...  This work was performed/conducted in the framework of the BIOSYS research project, Action KRIPIS, project No MIS-448301 (2013SE01380036) that was funded by the General Secretariat for Research and Technology  ...  , along with stable hairpin loop secondary structure (Hackenberg et al., 2009) miRdba Optimal alignment of candidate and known miRNA read profiles (Pundhir and Gorodkin, 2013) Non-coding RNA classification  ... 
doi:10.3389/fgene.2015.00188 pmid:26042150 pmcid:PMC4437211 fatcat:xp2o2hug3vfutjswlrnupc36ze

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing

Mariko Tsuchiya, Kojiro Amano, Masaya Abe, Misato Seki, Sumitaka Hase, Kengo Sato, Yasubumi Sakakibara
2016 Bioinformatics  
After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional  ...  Results: We developed an algorithm termed SHARAKU to align two read mapping profiles of nextgeneration sequencing outputs for non-coding RNAs.  ...  Erika Sasaki and Takashi Inoue (CIEA, Japan) for providing the common Marmoset sample.  ... 
doi:10.1093/bioinformatics/btw273 pmid:27307639 pmcid:PMC4908357 fatcat:vwnyqckvlfenhhva22iauqhyda

A Review on Recent Computational Methods for Predicting Noncoding RNAs

Yi Zhang, Haiyun Huang, Dahan Zhang, Jing Qiu, Jiasheng Yang, Kejing Wang, Lijuan Zhu, Jingjing Fan, Jialiang Yang
2017 BioMed Research International  
reads generated from next-generation RNA sequencing, and (4) RNA family specific methods, for example, methods specific for microRNAs and long noncoding RNAs.  ...  In the future, high efficient mapping technology and more intrinsic sequence features (e.g., motif and k-mer frequencies) and structure features (e.g., minimum free energy, conserved stem-loop, or graph  ...  Conflicts of Interest The authors declare that they have no conflicts of interest. Authors' Contributions  ... 
doi:10.1155/2017/9139504 pmid:28553651 pmcid:PMC5434267 fatcat:gwcnzcftrfgmpiaeepmqfrbogq