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Preview: Evolutionary Bioinformatics

Evolutionary Bioinformatics

An international, peer reviewed, open access journal focusing on evolutionary bioinformatics.  The journal aims to support understanding of organismal form and function through use of molecular, genetic, genomic and proteomic data by giving due consi


Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines


The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 1 ...

MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL


A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic distances between taxa. These methods have the com ...

A Modified Mean Gray Wolf Optimization Approach for Benchmark and Biomedical Problems


A modified variant of gray wolf optimization algorithm, namely, mean gray wolf optimization algorithm has been developed by modifying the position update (encircling behavior) equations of gray wolf optimization algorithm. The proposed variant has been tested on 23 standard benchmark well-known test functions (unimodal, multimodal, and fixed-dimension multimodal), and the performance of modifi ...

Hierarchical Association Coefficient Algorithm: New Method for Genome-Wide Association Study


Hierarchical association coefficient algorithm calculates the degree of association between observations and categories into a value named hierarchical association coefficient (HA-coefficient) between 0 for the lower limit and 1 for the upper limit. The HA-coefficient algorithm can be operated with stratified ascending categories based on the average of observations in each category. Th ...

Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis


The accurate estimation of nucleotide variability using next-generation sequencing data is challenged by the high number of sequencing errors produced by new sequencing technologies, especially for nonmodel species, where reference sequences may not be available and the read depth may be low due to limited budgets. The most popular single-nucleotide polymorphism (SNP) callers are designed to o ...

Complete Mitochondrial Genomes of the Cherskii’s Sculpin and Siberian Taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome


The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii’s sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected bet ...

Popmarker: Identifying Phylogenetic Markers at the Population Level


As phylogenomic approach becomes a common practice for constructing true bacterial phylogenies, it has become apparent that single molecular markers such as 16S ribosomal DNA often lead to misclassification of species. In this study, we present a program called Popmarker that uses the true species phylogeny and identifies a minimum set of molecular markers reflecting the bacterial evolution hi ...

Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments


High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVID ...

Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus , family


Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we de ...

RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes


Accumulated microarray data are used for assessing gene function by providing statistical values for co-expressed genes; however, only a limited number of Web tools are available for analyzing the co-expression of genes of Brassica rapa. We have developed a Web tool called RapaNet (, which is based on a data set of 143 ...

Genome-Wide Identification and Comparative Analysis of Albumin Family in Vertebrates


Albumins are the most well-known globular proteins, and the most typical representatives are the serum albumins. However, less attention was paid to the albumin family, except for the human and bovine serum albumin. To characterize the features of albumin family, we have mined all the putative albumin proteins from the available genome sequences. The results showed that albumin is widely distr ...

Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting


KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elem ...

Phylogenetic Analysis of Nuclear-Encoded RNA Maturases


Posttranscriptional processes, such as splicing, play a crucial role in gene expression and are prevalent not only in nuclear genes but also in plant mitochondria where splicing of group II introns is catalyzed by a class of proteins termed maturases. In plant mitochondria, there are 22 mitochondrial group II introns. matR, nMAT1, nMAT2, nMAT3, and nMAT4 proteins have been shown to be r ...

Performance of Hidden Markov Models in Recovering the Standard Classification of Glycoside Hydrolases


Glycoside hydrolases (GHs) are carbohydrate-active enzymes that assist the hydrolysis of glycoside bonds of complex sugars into carbohydrates. The current standard GH family classification is available in the CAZy database, which is based on the similarities of amino acid sequences and curated semi-automatically. However, with the exponential increase in data availability from genome sequences ...

Free-Living Enterobacterium 24613: Complete Genome Sequence and Metabolic Profiling


Pragia fontium is one of the few species that belongs to the group of atypical hydrogen sulfide-producing enterobacteria. Unlike other members of this closely related group, P. fontium is not associated with any known host and has been reported as a free-living bacterium. Whole genome sequencing and metabolic fingerprinting confirmed the phylogenetic position of P. fontium ...

A New Hybrid MGBPSO-GSA Variant for Improving Function Optimization Solution in Search Space


In this article, a newly hybrid nature-inspired approach (MGBPSO-GSA) is developed with a combination of Mean Gbest Particle Swarm Optimization (MGBPSO) and Gravitational Search Algorithm (GSA). The basic inspiration is to integrate the ability of exploitation in MGBPSO with the ability of exploration in GSA to synthesize the strength of both approaches. As a result, the presented approach has ...

Numericware i: Identical by State Matrix Calculator


We introduce software, Numericware i, to compute identical by state (IBS) matrix based on genotypic data. Calculating an IBS matrix with a large dataset requires large computer memory and takes lengthy processing time. Numericware i addresses these challenges with 2 algorithmic methods: multithreading and forward chopping. The multithreading allows computational routines to concurrently run on ...

Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting


Hybridization events generate reticulate species relationships, giving rise to species networks rather than species trees. We report a comparative study of consensus, maximum parsimony, and maximum likelihood methods of species network reconstruction using gene trees simulated assuming a known species history. We evaluate the role of the divergence time between species involved in a hybridizat ...

A Method to Categorize 2-Dimensional Patterns Using Statistics of Spatial Organization


We developed a measurement framework of spatial organization to categorize 2-dimensional patterns from 2 multiscalar biological architectures. We propose that underlying shapes of biological entities can be approached using the statistical concept of degrees of freedom, defining it through expansion of area variability in a pattern. To help scope this suggestion, we developed a mathematical ar ...

Discovery and Characterisation of Castlerea Virus, a New Species of Isolated in Australia


With advances in sequencing technologies, there has been an increase in the discovery of viruses that do not group with any currently described virus families. The newly described taxon Negevirus encompasses a group of viruses displaying an insect-specific phenotype which have been isolated from multiple host species on numerous continents. Using a broad-spectrum virus screening assay b ...

The Transposon Provides Messages That Yield Unique Profiles of Protein Isoforms and Acts Synergistically With to Enrich Proteome Complexity via Exonization


In exonization events, Ds1 may provide donor and/or acceptor sites for splicing after inserting into genes and be incorporated into new transcripts with new exon(s). In this study, the protein variants of Ds1 exonization yielding additional functional profile(s) were studied. Unlike Ds exonization, which creates new profiles mostly by incorporating flanking intron sequence ...

The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup


Clostridium haemolyticum is the causal agent of bacillary hemoglobinuria in cattle, goat, sheep, and ruminants. In this study, we report the first recorded human-infecting C. haemolyticum strain collected from an 18-year-old woman diagnosed with acute lymphoblastic leukemia. After failure of traditional techniques, only next-generation sequencing (NGS) technology in combination w ...



Gamisch A. Notes on the Statistical Power of the Binary State Speciation and Extinction (BiSSE) Model. Evolutionary Bioinformatics 2016;12:165–174. (Original DOI: 10.4137/EBO.S39732) ...