Evolutionary bioinformatics

Two different approaches can be used in phylogenomics: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid...

We propose a simple, sensitive measure of synonymous codon usage bias, the Relative Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and unbiased regions, compared with the widely used Codon Adaptation Index (CAI). CAI is a geometric mean of the relative usage of codons in...

RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting...

Certain species of the fungal genus Trichoderma are potent mycoparasites and are used for biological control of fungal diseases on agricultural crops. In Trichoderma, whole-genome sequencing reveal between 20 and 36 different genes encoding chitinases, hydrolytic enzymes that are involved in the mycoparasitic attack. Sequences of Trichoderma chitinase genes chi18-5,...

The sizes of the protein databases are growing rapidly nowadays, thus it becomes increasingly important to cluster protein sequences only based on sequence information. In this paper we improve the similarity measure proposed by Kelil et al, then cluster sequences using the Affinity propagation (AP) algorithm and provide a method...

Achievement of the best balance between the accuracy and efficiency is always an important issue when searching a tree space of large data sets. In the 5th issue in 2009, Rodrigo et al used bootstrapped topologies as fixed genealogies to distribute an MCMC analysis across a cluster of computers, resulting...

The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified 207 ETS genes which encode 321 ETS TFs from ten animal species. Of the 321 ETS TFs, 155...

The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified 207 ETS genes which encode 321 ETS TFs from ten animal species. Of the 321 ETS TFs, 155...

In the post-genomic era the complex problem of evolutionary biology can be tackled from the top-down, the bottom-up, or from the middle-out. Given the emergent and contingent nature of this process, we have chosen to take the latter approach, both as a mechanistic link to developmental biology and as a...

Negative selection against protein instability is a central influence on evolution of proteins. Protein stability is maintained over evolution despite changes in underlying sequences. An empirical all-site stability-based model of evolution was developed to focus on the selection of residues arising from their contributions to protein stability. In this model,...

Coalescent-based Bayesian Markov chain Monte Carlo (MCMC) inference generates estimates of evolutionary parameters and their posterior probability distributions. As the number of sequences increases, the length of time taken to complete an MCMC analysis increases as well. Here, we investigate an approach to distribute the MCMC analysis across a cluster...

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable...

Evolutionary changes in gene expression account for most phenotypic differences between species. Advances in microarray technology have made the systematic study of gene expression evolution possible. In this study, gene expression patterns were compared between human and mouse genomes using two published methods. Specifically, we studied how gene expression evolution...

Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it...

Homologous recombination is a pervasive biological process that affects sequences in all living organisms and viruses. In the presence of recombination, the evolutionary history of an alignment of homologous sequences cannot be properly depicted by a single bifurcating tree: some sites have evolved along a specific phylogenetic tree, others have...

Ergot alkaloids are indole-derived mycotoxins that are important in agriculture and medicine. Ergot alkaloids are produced by a few representatives of two distantly related fungal lineages, the Clavicipitaceae and the Trichocomaceae. Comparison of the ergot alkaloid gene clusters from these two lineages revealed differences in the relative positions and orientations...

Background: In vertebrates the “SONIC HEDGEHOG” signalling pathway has been implicated in cell-fate determination, proliferation and the patterning of many different cell types and organs. As the GLI family members (GLI1, GLI2 and GLI3) are key mediators of hedgehog morphogenetic signals, over the past couple of decades they have...

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the...

Phylogenetic methods have revolutionised evolutionary biology and have recently been applied to studies of linguistic and cultural evolution. However, the basic comparative data on the languages of the world required for these analyses is often widely dispersed in hard to obtain sources. Here we outline how our Austronesian Basic Vocabulary...

The genome of the hepatitis C virus (HCV) exhibits a high genetic variability. This remarkable heterogeneity is mainly attributed to the gradual accumulation of mutational changes, whereas the contribution of recombination events to the evolution of HCV remains controversial so far. While performing phylogenetic analyses including a large number of...

The adequacy of substitution matrices to model evolutionary relationships between amino acid sequences can be numerically evaluated by checking the mathematical property of triangle inequality for all triplets of residues. By converting substitution scores into distances, one can verify that a direct path between two amino acids is shorter than...

Haseeb A. Khan, Ibrahim A. Arif, Ali H. Bahkali, Ahmad H. Al Farhan and Ali A. Al Homaidan Molecular Fingerprinting and Biodiversity Unit, Prince Sultan Research Chair Program in Environment and Wildlife, College of Science, King Saud University, Riyadh, Saudi Arabia. Abstract This investigation...

Marc Thuillard Belimo Automation AG, CH-8340 Hinwil, Switzerland Abstract Minimum contradiction matrices are a useful complement to distance-based phylogenies. A minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix Yni,j . A matrix element corresponds to the distance from a...

Arnaud Le Rouzic1 and José M. Álvarez-Castro2 1Center for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway. 2Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. Abstract Determining the genetic architecture of complex traits is a necessary step to understand phenotypic changes...

Saurav Singh and Dennis P. Wall Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115. Abstract A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will...

Saurav Singh and Dennis P. Wall Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115. Abstract A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will...

Najl V. Valeyev1,4, A. Kristina Downing1, John Sondek2 and Charlotte Deane3 1Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K. 2Department of Pharmacology, University of North Carolina, 27599-7365, U.S.A. 3Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, U.K. 4Current address:...

R. Henrik Nilsson1, Erik Kristiansson2, Martin Ryberg1, Nils Hallenberg1 and Karl-Henrik Larsson1 1Department of Plant and Environmental Sciences, University of Gothenburg, Box  461, 405 30 Göteborg, Sweden. 2Mathematical Statistics, Chalmers University of Technology/Department of Zoology, University of Gothenburg, 412 96 Göteborg, Sweden. Abstract The internal transcribed spacer...

Wei Zhang1 and M. Eileen Dolan1,2,3 1Section of Hematology/Oncology, Department of Medicine, 2Committee on Clinical Pharmacology and Pharmacogenomics, 3Cancer Research Center, The University of Chicago, IL 60637, U.S.A. Abstract Though debates exist on the early human evolutionary models such as the “Out of Africa” theory, which...