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DART: a fast and accurate RNA-seq mapper with a partitioning strategy

Hsin-Nan Lin, Wen-Lian Hsu, Bonnie Berger
2017 Bioinformatics  
Results: We proposed a novel RNA-seq de novo mapping algorithm, call DART, which adopts a partitioning strategy to avoid the extension step.  ...  Most read mappers follow the conventional seed-and-extend strategy to deal with inexact matches for sequence alignment. However, the extension is much more time consuming than the seeding step.  ...  We would also like to thank Thasso Griebel et al. for developing the RNA-seq simulator.  ... 
doi:10.1093/bioinformatics/btx558 pmid:28968831 pmcid:PMC5860201 fatcat:kyx6ejl6nnedhkizbnw3kzcqvm

TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks

Huey Eng Chua, Sourav S Bhowmick, Jie Zheng, Jonathan Wren
2017 Bioinformatics  
-T.Wu and B.A utility maximizing and privacy preserving approach for protecting kinship in genomic databases G.Kale, E.Ayday and O.Tastan Sequence analysis DART: a fast and accurate RNA-seq mapper with  ...  a partitioning strategy H.  ... 
doi:10.1093/bioinformatics/btx600 pmid:29028982 fatcat:xgf3ijfm4nfxnn3gl3y3zxfcum

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.  ...  Importantly, computational algorithms have evolved and diversified in accordance with technological advances, leading to todays diverse array of bioinformatics tools.  ...  DART: a fast and accurate RNA-seq mapper with a partitioning strategy. Bioinformatics vol. 34 190-197 (2018). 143. Li, H. Minimap2: pairwise alignment for nucleotide sequences.  ... 
arXiv:2003.00110v3 fatcat:3l3ad4z5xfhjxoo7snaskartxi

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.  ...  Our review provides a systemic overview of RNA-seq technology and 235 available RNA-seq tools across various domains published from 2008 to 2020, discussing the interdisciplinary nature of bioinformatics  ...  Patro for his valuable comments and suggestions on the manuscript. Competing Interests The authors declare no competing interests. References  ... 
arXiv:2010.02391v3 fatcat:krgm7uzmibdlfh2ylgqxmnh2qu