1. Introduction
  2. IsoInfer is a C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information. This version of IsoInfer uses a unified way to handle different types of short reads with different lengths. The source code is provided for non-commercial usage. We appologize for the unavailability of the Windows and Mac versions of this program at the present time.

  3. All Versions
  4. The following links lead to the source packages, compilation details, manual and examples.
    Version Date Modifications
    IsoInfer V0.9.1 9/28/2010 A bug in V0.9 is fixed. This bug generates duplicated predictions
    IsoInfer V0.9 8/18/2010 Expression level of predicted isoforms are outputed.
    The inference strategy is modified when TSS/PAS information is missing.
    New strategy adopts a similar normalization step of Scripture.
    IsoInfer V0.8.2 7/25/2010 When TSS/PAS information is missing (i.e. parameter -tsspas is not specified),
    IsoInfer still works.
    IsoInfer V0.8.1 7/15/2010 Customized distribution type is supported.
    A bug in calculating virtual length for var single-end reads is fixed
    IsoInfer V0.8 7/3/2010 A more friendly interface is provided. The noise reduction functionality is added.
    IsoInfer V0.7 6/24/2010 Version 0.6 outputs only prediction results on genes with at least 8 known isoforms.
    This version gives prediction results of all genes by default.
    IsoInfer V0.6 6/10/2010 Bugs fixed
    IsoInfer V0.5 5/31/2010 This version proposed a unified way of handling single-end and paired-end short reads with different lengths and distributions.
    Bugs fixed
    IsoInfer V0.4 1/20/2010 Bugs fixed

  5. References
  6. Jianxing Feng, Wei Li and Tao Jiang. Inference of isoforms from short sequence reads (Extended Abstract). 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Lisbon, Portugal, April 25-28, 2010

    The full version of this paper is here: isoinfer_full.pdf

  7. Questions and Feedback
  8. Please email to: