TopHat

TopHat is a bioinformatics software application used for identifying splice junctions in RNA-Seq data. It was developed by the Center for Computational Biology at Johns Hopkins University. TopHat uses the ultra-high-throughput short read aligner Bowtie to align reads to a genome, and then analyzes the mapping results to identify splice junctions between exons.

Overview

TopHat is a program that aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the Center for Computational Biology at Johns Hopkins University and the Bioinformatics team at the University of Maryland.

Methodology

TopHat first aligns RNA-Seq reads to the genome using Bowtie, and then identifies the exons and splice junctions. The software uses a novel method to align reads that span two or more exons of a gene. The method involves splitting the read into segments and aligning them independently to the genome in order to identify potential splice sites.

Applications

TopHat is widely used in the field of bioinformatics for the analysis of RNA-Seq data. It is particularly useful for the study of alternative splicing events, which are believed to play a key role in the complexity of the human transcriptome.

See also

• RNA-Seq
• Bioinformatics
• Center for Computational Biology
• Bowtie (sequence analysis)

References

TopHat Resources
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