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TopHat (bioinformatics)

From Wikipedia, the free encyclopedia

TopHat is a bioinformatic sequence analysis package tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies (e.g. RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo.

TopHat was originally developed in 2009 by Cole Trapnell, Lior Pachter and Steven Salzberg at the Mathematics Department, UC Berkeley and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.[1] Trapnell later moved to Genome Sciences Department at the University of Washington. Currently TopHat is a collaborative effort between Cole Trapnell at the University of Washington and Daehwan Kim and Steven Salzberg in the Center for Computational Biology at Johns Hopkins University who together in 2013 also came up with TopHat2 which does accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.[2]

See also


  1. ^ Trapnell, C.; Pachter, L.; Salzberg, S. L. (16 March 2009). "TopHat: discovering splice junctions with RNA-Seq". Bioinformatics. 25 (9): 1105–1111. doi:10.1093/bioinformatics/btp120. PMC 2672628Freely accessible. PMID 19289445. 
  2. ^ Kim, Daehwan; Pertea, Geo; Trapnell, Cole; Pimentel, Harold; Kelley, Ryan; Salzberg, Steven L (2013). "TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions". Genome Biology. 14 (4): R36. doi:10.1186/gb-2013-14-4-r36. PMC 4053844Freely accessible. PMID 23618408. 

External links

This page was last edited on 27 August 2017, at 23:59.
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