Related Experiment Video
Updated: Jan 19, 2026
An R-Based Landscape Validation of a Competing Risk Model
Published on: September 16, 2022
Statistical compression of protein sequences and inference of marginal probability landscapes over competing
Dinithi Sumanaweera1, Lloyd Allison1, Arun S Konagurthu1
1Faculty of Information Technology, Monash University, Clayton, VIC, Australia.
Abstract:
The information criterion of minimum message length (MML) provides a powerful statistical framework for inductive reasoning from observed data. We apply MML to the problem of protein sequence comparison using finite state models with Dirichlet distributions. The resulting framework allows us to supersede the ad hoc cost functions commonly used in the field, by systematically addressing the problem of arbitrariness in alignment parameters, and the disconnect between substitution scores and gap costs. Furthermore, our framework enables the generation of marginal probability landscapes over all possible alignment hypotheses, with potential to facilitate the users to simultaneously rationalize and assess competing alignment relationships between protein sequences, beyond simply reporting a single (best) alignment. We demonstrate the performance of our program on benchmarks containing distantly related protein sequences.
Availability And Implementation:
The open-source program supporting this work is available from: http://lcb.infotech.monash.edu.au/seqmmligner.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
05:37An R-Based Landscape Validation of a Competing Risk Model
01:14Probability in Statistics
An example of a simple event is a coin toss. The result of a coin toss is either a head or a tail. Here, head and tail are two simple events. These two simple events make up the sample space. Further, the probability of an event occurring falls within the range of 0 to 1. The probability of an...
06:34Finite Element Modeling for the Simulation of the Quasi-Static Compression of Corrugated Tapered Tubes
16:02Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
01:16Statistical Inference Techniques in Hypothesis Testing: Parametric Versus Nonparametric Data
Parametric statistics, as the name suggests, assumes that data follow a specific distribution, often a normal distribution. This assumption enables robust hypothesis testing and estimation. Parametric methods, like the Student's t-test or Goodness-of-fit test, are frequently employed in biostatistics due to their robustness. For instance,...
11:10Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3