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PMID: 21835007 Published · epublish English Journal Article Research Support, N.I.H., Extramural

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

Genome biology ·Vol. 12 ·No. 8 ·2011-08-11 ·Pages R72

Kim D, Salzberg SL

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/.

MeSH Terms
Algorithms Base Sequence Breast Neoplasms/metabolism Cell Line, Tumor Female Gene Expression Profiling/methods Gene Fusion Humans Male Molecular Sequence Data Prostatic Neoplasms/metabolism Sequence Analysis, RNA Software
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Kim Daehwan
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. [email protected]
Salzberg Steven L
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2011-12-8-r72
Email
[email protected]
Published
2011-08-11
Epub
2011-00-11
Pages
R72
Language
English
Region
England
NLM ID
100960660
PMCID
PMC3245612
Subset
IM
Grants
NHGRI NIH HHS · R01 HG006677 · United States
NHGRI NIH HHS · R01-HG006102 · United States
NHGRI NIH HHS · R01 HG006102-02 · United States
NHGRI NIH HHS · R01 HG006677-12 · United States
NLM NIH HHS · R01-LM006845 · United States
NHGRI NIH HHS · R01 HG006102 · United States
NHGRI NIH HHS · R01 HG006677-13 · United States
NIGMS NIH HHS · R01 GM083873 · United States
NHGRI NIH HHS · R01 HG006102-01 · United States
External Links
PubMed source DOI: 10.1186/gb-2011-12-8-r72 PMC Full Text View journal details
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