In the post-genome era, insufficient functional annotation of predicted genes greatly restricts the potential of mining genome data. We demonstrate that an evolutionary approach, which is independent of functional annotation, has great potential as a tool for genome analysis. We chose the genome of a model filamentous fungus Neurospora crassa as an example. Phylogenetic distribution of each pre...

In the computational biology and taxonomy, to construct phylogenetic tree is an important problem. A phylogenetic tree can represent the relationship and histories for a set of species and helpful for biologists to observe existent species. One of popular model is ultrametric tree, and it assumed the evolution rate is constant. UPGMA is one of well-known ultrametric tree algorithm. However, UPG...

A cDNA that encodes protein disulfide isomerase was isolated from Bombyx mori (bPDI), in which an open reading frame of 494 amino acids contained two PDI-typical thioredoxin active sites of WCGHCK and an ER retention signal of the KDEL motif at its C-terminal. The bPDI protein shared less than 55% of the amino acid sequence homology with other reported PDIs. bPDI is most genetically similar to ...

We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein fami...

For many years, numerous investigators have been trying to better understand the evolution of the vertebrates, especially the phylogeny of the tetrapods or land vertebrates. Most of the information comes from paleontological or anatomic work. Nucleic acid and protein sequence analyses are very recent techniques and are providing new information on the subject (Bernardi et al., 1992). The relati...

The epidemiology of non-typeable Haemophilus influenzae (NTHi) remains poorly understood. We therefore sought to determine the genetic relationship of 25 NTHi isolated from various states in Malaysia using multilocus sequence typing (MLST). The majority of isolates were obtained from sputum. There were 24 novel sequence types (STs). Eight isolates were single-locus variants, the remainder being...

Phylogenetic networks model evolutionary histories in the presence of non-treelike events such as hybrid speciation and horizontal gene transfer. In spite of their widely acknowledged importance, very little is known about phylogenetic networks, which have so far been studied mostly for specific datasets. Even when the evolutionary history of a set of species is non-treelike, individual genes i...

Anti-N-methyl-d-aspartate (Anti-NMDA) receptor encephalitis is an acute autoimmune neurological disorder. The cause of this disease is often unknown, and previous studies revealed that it might be caused by a virus, vaccine or tumor. It occurs more often in females than in males. Several cases were reported to be related to vaccination such as the H1N1 vaccine and tetanus/diphtheria/pertussis a...

SSR (simple sequence repeats) are ubiquitously abundant in genomes. In organellar mitochondrial genome of animals, its distribution, size dynamics and effectiveness for phylogenetic relationship have not been understood. Present investigation reveals organisation of SSR in genic and intergenic region, its length and repeat motif dynamics, extent of conservation of flanking regions, appropriaten...

Much attention has been payed to tree shrews for their close phylogenetic relationship with primates, small size, and short reproductive cycle. Especially, they are considered as excellent experiential animals for medicine or/and disease research. A nucleotide sequence encoding neuropeptide Y(NPY) precursor has been cloned from the cDNA library of Tupaia belangeri chinensis. Sequence alignment ...