BACKGROUND K+ and Na+ channel toxins constitute a large set of polypeptides, which interact with their ion channel targets. These polypeptides are classified in two different structural groups. Recently a new structural group called birtoxin-like appeared to contain both types of toxins has been described. We hypothesized that peptides of this group may contain two conserved structural motifs i...

Porcine epidemic diarrhea virus (PEDV) is a positive-sense RNA virus that causes infectious gastroenteritis in pigs. Following a PED outbreak that occurred in China in 2010, the disease was identified for the first time in the United States in April 2013, and was reported in many other countries worldwide from 2013 to 2014. As a novel approach to elucidate the epidemiological relationship betwe...

Superoxide dismutase (SOD) is a crucial metal-containing enzyme that plays vital role in catalyzing the dismutation of superoxide anions, converting them into molecular oxygen and hydrogen peroxide, essential for enhancing plant stress tolerance. We identified 8 SOD genes (4 CSODs, 2 FSODs, MSODs) cassava. Bioinformatics analyses provided insights chromosomal location, phylogenetic relationship...

The basic leucine zipper (bZIP) transcription factors play important regulatory roles, influencing plant growth and responses to environmental stresses. In the present study, 132 bZIP genes identified in tobacco genome were classified into 11 groups with Arabidopsis tomato members, based on results of a phylogenetic analysis. An examination gene structures conserved motifs revealed relatively e...

We present a new probabilistic model of evolution of RNA-, DNA-, or protein-like sequences and a tool rose that implements this model. By insertion, deletion and substitution of characters, a family of sequences is created from a common ancestor. During this artificial evolutionary process, the ’~true" history is logged and the "correct" multiple sequence alignment is ereated simultaneously. We...

For both the computational biologist and the research biologist, the use of multiple sequence alignment (MSA) programs to simultaneously align multiple sequences of nucleic acids or proteins has become de rigueur. Successful alignments are used in a number of applications, such as (1) phylogenetic analysis, as a predictor of evolutionary relationships; (2) identifying conserved motifs and domai...

Computer analysis of complete prokaryotic genomes shows that microbial proteins are in general highly conserved — ~70% of them contain ancient conserved regions. This allows us to delineate families of orthologs across a wide phylogenetic range and, in many cases, predict protein functions with considerable precision. Sequence database searches using newly developed, sensitive algorithms result...

We present a new probabilistic model of evolution of RNA-, DNA-, or protein-like sequences and a tool rose that implements this model. By insertion, deletion and substitution of characters, a family of sequences is created from a common ancestor. During this artificial evolutionary process, the "true" history is logged and the "correct" multiple sequence alignment is created simultaneously. We ...

Interest in the use of low-copy nuclear genes for phylogenetic analyses of plants has grown rapidly, because highly repetitive genes such as those commonly used are limited in number. Furthermore, because low-copy genes are subject to different evolutionary processes than are plastid genes or highly repetitive nuclear markers, they provide a valuable source of independent phylogenetic evidence....