SnowShoes-FTD is a bioinformatics tool to identify fusion transcripts from paired-end transcriptome sequencing data. The tool employs multiple steps of false positive filtering and nominates the fusion candidates with high confidence (approaching 100% true positive rate). The unique features of SnowShoes-FTD include: (i) the ability to discover multiple fusion isoforms in which the two gene partners give rise to transcripts with different junctions; (ii) prediction of potential fusion mechanisms including inversion, translocation, and/or interstitial deletions; (iii) identification of whether the junction point in a fusion transcript occurs at the boundaries of known exons which implies the fusion events might have happened inside an intron in DNA and transcribed to the fusion transcript.
Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research
Please contact the author, Yan W. Asmann, Ph.D. firstname.lastname@example.org
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Nucleic Acids Res. 2011 Aug;39(15):e100. Epub 2011 May 27.
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.