Corpus ID: 16011939

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data

@article{Sacomoto2014EfficientAF,
  title={Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data},
  author={Gustavo Sacomoto},
  journal={ArXiv},
  year={2014},
  volume={abs/1406.6047}
}
  • Gustavo Sacomoto
  • Published 2014
  • Mathematics, Computer Science, Biology
  • ArXiv
  • In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the idea that each variant corresponds to a recognizable pattern, a bubble, in a de Bruijn graph constructed from the RNA-seq reads, we propose a general model for all variants in such graphs. We then introduce an exact method, called KisSplice, to extract… CONTINUE READING

    Citations

    Publications citing this paper.

    References

    Publications referenced by this paper.
    SHOWING 1-10 OF 153 REFERENCES

    KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

    VIEW 2 EXCERPTS

    Complete Alternative Splicing Events Are Bubbles in Splicing Graphs

    Full-length transcriptome assembly from RNA-Seq data without a reference genome.

    VIEW 11 EXCERPTS
    HIGHLY INFLUENTIAL