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PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data

Yanju Zhang, Eric-Wubbo Lameijer, Peter A. C. 't Hoen, Zemin Ning, P. Eline Slagboom, Kai Ye
2012 Computer applications in the biosciences : CABIOS  
Results: We developed PASSion, a pattern growth algorithm-based pipeline for splice site detection in paired-end RNA-Seq reads.  ...  Motivation: RNA-seq is a powerful technology for the study of transcriptome profiles that uses deep-sequencing technologies.  ...  ACKNOWLEDGEMENTS We thank Dr Hannes Ponstingl for his advices on the use of SMALT and Erik van den Akker for his comments on the manuscript. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btr712 pmid:22219203 pmcid:PMC3278765 fatcat:iwrs4zyby5cajgbpupdvau524i

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

Jie Wu, Olga Anczuków, Adrian R. Krainer, Michael Q. Zhang, Chaolin Zhang
2013 Nucleic Acids Research  
Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads.  ...  A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions.  ...  ACKNOWLEDGEMENTS We would like to thank Michael Schatz and Martin Akerman for critical reading of the manuscript, and members of the Krainer, Zhang and Robert Darnell labs for helpful discussion.  ... 
doi:10.1093/nar/gkt216 pmid:23571760 pmcid:PMC3664805 fatcat:xd25ox2gsrb2dgtsn43avtcdli

UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing

Paul D. Burns, Yang Li, Jian Ma, Mark Borodovsky
2013 Nucleic Acids Research  
To improve detection of splice junctions, TrueSight uses information on statistical patterns of nucleotide ordering in intronic and exonic DNA.  ...  Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem.  ...  ACKNOWLEDGEMENTS We are very grateful to Alexandre Lomsadze for valuable technical assistance. We thank Susan M.E. Smith for useful comments.  ... 
doi:10.1093/nar/gkt1141 pmid:24259430 pmcid:PMC3936741 fatcat:cqjcgz342vcofl6txuex4saena

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity

Bishakha Roy, Larisa M. Haupt, Lyn R. Griffiths
2013 Current Genomics  
Our ability to determine and predict AS is important as disorders in splicing patterns may lead to abnormal splice variants resulting in genetic diseases.  ...  Microarrays and deep sequencing approaches also aid in the detection of splicing events.  ...  PASSion is a pattern growth algorithm-based pipeline useful in the detection of splice sites in paired-end RNA-Seq reads and can detect junctions that do not have known splicing motifs, which cannot be  ... 
doi:10.2174/1389202911314030004 pmid:24179441 pmcid:PMC3664468 fatcat:h7pkjfvxezauznlx3dthpyf2ce

RNA-seq data science: From raw data to effective interpretation [article]

Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin (+4 others)
2021 arXiv   pre-print
RNA-seq is a method of analyzing the RNA content of a sample using the modern sequencing platforms.  ...  RNA-seq analysis enables the probing of genes and corresponding transcripts which is essential for answering important biological questions, such as detecting novel exons, transcripts, gene expressions  ...  Patro for his valuable comments and suggestions on the manuscript. Competing Interests The authors declare no competing interests. References  ... 
arXiv:2010.02391v3 fatcat:krgm7uzmibdlfh2ylgqxmnh2qu

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

Y. Zhang, K. Chen, S. A. Sloan, M. L. Bennett, A. R. Scholze, S. O'Keeffe, H. P. Phatnani, P. Guarnieri, C. Caneda, N. Ruderisch, S. Deng, S. A. Liddelow (+5 others)
2014 Journal of Neuroscience  
We generated a transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type.  ...  For example, our data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the  ...  PCR products were detected from neuron, astrocyte, and whole-brain samples in patterns predicted by the RNA-Seq data.  ... 
doi:10.1523/jneurosci.1860-14.2014 pmid:25186741 pmcid:PMC4152602 fatcat:scqxcsocdfa23hn7ihjaes4uui

EMBnet.journal 19 Suppl. A

EMBnet Journal
2013 EMBnet journal  
* Kay Nieselt: Automated transcription start site prediction for comparative comparative * Oskar Erik Karlsson: Viral Metagenomics -New applications for the broad-range detection  ...  veterinary and public health settings. * Ignacio Blanquer Blanquer: Supporting NGS pilelines in the cluod. * Luca Pireddu: Automated and traceable processing for large-scale high-throughput sequencing  ...  Acknowledgements Research carried out in the context of this study has been funded by the EU DICODE (Mastering Data-Intensive Collaboration and Decision Making) Collaborative Project (FP7, ICT-2009.4.3  ... 
doi:10.14806/ej.19.a.689 fatcat:2xs4bsifarfipopojjerizk3ce

Technology dictates algorithms: Recent developments in read alignment [article]

Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums (+4 others)
2020 arXiv   pre-print
Our review provides a survey of algorithmic foundations and methodologies across 107 alignment methods published between 1988 and 2020, for both short and long reads.  ...  Aligned reads are essential for answering important biological questions, such as detecting mutations driving various human diseases and complex traits as well as identifying species present in metagenomic  ...  Although those tools can detect splicing junctions within their algorithm, it is possible to supply known gene annotation to increase the accuracy of a spliced alignment.  ... 
arXiv:2003.00110v3 fatcat:3l3ad4z5xfhjxoo7snaskartxi

Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa

María Gómez-Lozano, Rasmus Lykke Marvig, Søren Molin, Katherine S. Long
2012 Environmental Microbiology  
In sections 3.12 to 3.17, we describe a high-throughput bioinformatics pipeline for the analysis of RNA-Seq.  ...  Also probe-based methods cannot discriminate between different mRNA isoforms or define transcript borders and splice junctions with high resolution.  ... 
doi:10.1111/j.1462-2920.2012.02759.x pmid:22533370 fatcat:swk7fotaxfd4vaqgpguq52xprq

Programme Booklet Of The 11Th Iscb Student Council Symposium, Dublin, 2015 [article]

Mehedi Hassan, R Gonzalo Parra
2015 Zenodo  
This is a booklet containing programme of the day of the 11th ISCB Student Council Symposium, Dublin, 10 July 2015. This also contains all the abstracts of works presented on the day.  ...  For automated annotation of the whole genome, we are using ab initio software trained with paired-end RNA-Seq data from ten bat tissues.  ...  The development of novel high-throughput sequencing methods for RNA (RNA-Seq) provided a very powerful mean to study alternative splicing under multiple conditions at unprecedented depth.  ... 
doi:10.5281/zenodo.1253018 fatcat:b75h2xdwmralzfqdhs6jd6k4vm

Regulation of splicing networks in neurodevelopment

Sabastien Matthieu Weyn-Vanhentenryck
Alternative splicing of pre-mRNA is a critical mechanism for enabling genetic diversity, and is a carefully regulated process in neuronal differentiation.  ...  This work tests the hypothesis that RBP-RNA interactions are critical for regulating timed and coordinated alternative splicing changes during neurodevelopment and that these splicing changes are in turn  ...  RNA-Seq data read mapping and junction detection.  ... 
doi:10.7916/d8sr0bzf fatcat:qjbbk4x5enbk5ktmpzkci2z27i


Michael Anthony Gildea
To this end, I developed multiplexed primer extension sequencing (MPE-seq); a targeted RNA sequencing method that increases precision in genome-wide quantification of splicing isoforms and allows for the  ...  Abstract The study of pre-mRNA splicing has been greatly aided by the advent of RNA sequencing (RNA-seq), which enables the genome-wide detection of discrete splice isoforms.  ...  Data Analysis In the following sections we describe a general pipeline for MPE-seq data analysis and suggest publicly available software packages for each step.  ... 
doi:10.7298/cn5y-x954 fatcat:pb435vidk5fznftt7xgot4home

Abstracts Submitted for Presentation at the 2012 APS Annual Meeting

2012 Phytopathology  
Around one billion paired-end Illumina Hi-Seq reads were generated; the majority of them were mapped uniquely to one location in the reference genome.  ...  Data analysis pipelines were developed to classify sequences down to the species level using public data and in-house reference data.  ...  Non-degenerate primers were then designed for both idiomorphs based on sequence data of isolates from the PNW and Europe.  ... 
doi:10.1094/phyto-102-7-s4.1 fatcat:pwsd2yi2s5f33c7x2i6gc4bzca

Secondary structural analysis of human lncRNAs

Yizhu Lin
I first developed Mod-seeker, an automatic data analysis pipeline for Mod-seq(5, 6).  ...  To overcome theseconstraints, we developed a novel method for high-throughput probing of RNA structure using massively parallel sequencing (Mod-seq (5)).  ...  Andrea Berman for sharing Chapter 3 Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture  ... 
doi:10.1184/r1/7182998 fatcat:x5k5i7megvc7hlxdt6zlpk7624

The role of the 3' untranslated region in breast cancer

Extension and validation of the work in this thesis may one day lead to a better test for breast cancer outcome.  ...  Our genes and the way in which our genetic code is read makes us who we are. Unfortunately, our genetic code can be altered or misinterpreted in cancer.  ...  Acknowledgements We thank members of the Beilharz Lab for constructive comment on the manuscript.  ... 
doi:10.26180/5bdfa95fa2fbf fatcat:uvo6jnzxrbeepocdjc5udsqh5i
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