Online exercise for the design and simulation of PCR and PCR-RFLP experiments

[EN] Background: Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings: An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes,compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions: The exercise is freely available at http://insilico.ehu.es/edu.

An R package for permutations, Mallows and Generalized Mallows models

[EN]Probability models on permutations associate a probability value to each of the permutations on n items. This paper considers two popular probability models, the Mallows model and the Generalized Mallows model. We describe methods for making inference, sampling and learning such distributions, some of which are novel in the literature. This paper also describes operations for permutations, with special attention in those related with the Kendall and Cayley distances and the random generation of permutations. These operations are of key importance for the efficient computation of the operations on distributions. These algorithms are implemented in the associated R package. Moreover, the internal code is written in C++.