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TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

ABSTRACT: TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/.

SUBMITTER: Kim D

PROVIDER: S-EPMC3245612 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

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TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Kim Daehwan D Salzberg Steven L SL

Genome biology 20110811 8

TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated s ...[more]

PMID: 21835007

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