ExaLT – Accurate Genome-Wide Survival Analysis

ExaLT

:: DESCRIPTION

Current implementations of the log-rank test (R survdiff, SAS LIFETEST, etc.) are based on an asymptotic approximation for the distribution of the log-rank statistic that is not appropriate when the two populations to be compared are unbalanced, as it is the case when testing the association of a mutation with survival in genomic studies. This asymptotic approximation results in p-values that can be very different from the exact p-values, up to 7 orders of magnitude, and a large number of false discoveries are reported because of this difference.

ExaLT (Exact Log-rank Test) is a method to compute a conservative approximation of the exact p-value. In particular, the method computes the p-value for the exact permutational p-value, that is more appropriate for testing the association of mutations with survival.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler / R package

:: DOWNLOAD

 ExaLT

:: MORE INFORMATION

Citation

Accurate computation of survival statistics in genome-wide studies.
Vandin F, Papoutsaki A, Raphael BJ, Upfal E.
PLoS Comput Biol. 2015 May 7;11(5):e1004071. doi: 10.1371/journal.pcbi.1004071.

F. Vandin, A. Papoutsaki, B.J. Raphael, E.Upfal (2013)
Genome-Wide Survival Analysis of Somatic Mutations in Cancer.
17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013).

ExAlt 1.0 – Alternative Exon Isoform Prediction

ExAlt 1.0

:: DESCRIPTION

ExAlt is a software program designed to predict alternatively spliced overlapping exons in genomic sequence. The program works in several ways depending on the available input. ExAlt can use information about existing gene structure as well as sequence conservation to improve the precision of its predictions. ExAlt can also make predictions when only a single genomic sequence is available.

::DEVELOPER

Jonathan E. Allen at the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ExAlt

:: MORE INFORMATION

The ExAlt software is OSI Certified Open Source Software.

Citation:

J. E. Allen and S. L. Salzberg. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.Algorithms for Molecular Biology, 1:14, 2006.