classify specified organisms taxonomically, determine the origins of proteinencoding genes, and infer how proteins function based on their conserved sequence motifs. Typically, phylogenic analysis involves two steps: constructing a phylogenetic tree or network based on the given biosequences and deriving biological information from the tree or network. Many computational methods have been devel...

despite routine vaccination programs against newcastle disease (nd), sporadic cases have occasionally occurred that remain a constant threat to commercial poultry. ten isolates of newcastle disease viruses (ndv) from infected broiler chicken cases were obtained from various locations in fars province during 2009-2011 and genetically analyzed using reverse transcription polymerase chain reaction...

RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeat...

Phylogenetic methods have shown promise in understanding the development of broadly neutralizing antibody lineages (bNAbs). However, the mutational process that generates these lineages, somatic hypermutation, is biased by hotspot motifs which violates important assumptions in most phylogenetic substitution models. Here, we develop a modified GY94-type substitution model that partially accounts...

How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the ex...

It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a phylogenetic distance is introduced and the corresponding distance matrix between proteomes is constructed. From the distance matrix a phylogenetic tree is ...

Current phylogenetic analysis of the flavivirus genus has identified a group mosquito-borne viruses for which vertebrate hosts are currently unknown. Here we report identification novel member this from peridomestic rodent species ( Sundamys muelleri ) collected in Sarawak, Malaysia 2016. We propose to name Batu Kawa virus after location it was identified, with abbreviation BKWV. Characterizati...

The identification of sequence motifs is a fundamental method for suggesting good candidates for biologically functional regions such as promoters, splice sites, binding sites, etc. We investigate the following approach to identifying motifs: given a collection of orthologous sequences from multiple species related by a known phylogenetic tree, search for motifs that are well conserved (accordi...