High-throughput sequencing of 16S rRNA gene amplicons has revolutionized the capacity and depth of microbial community profiling. Several sequencing platforms are available, but most phylogenetic studies are performed on the 454-pyrosequencing platform because its longer reads can give finer phylogenetic resolution. The Pacific Biosciences (PacBio) sequencing platform is significantly less expe...

Phylogenetic profiling is a well-established approach for predicting gene function based on patterns of gene presence and absence across species. Much of the recent developments have focused on methodological improvements, but relatively little is known about the effect of input data size on the quality of predictions. In this work, we ask: how many genomes and functional annotations need to be...

results comparative analysis of predicted amino acids in the phylogenetic tree showed high similarity between c. glabrata and s cerevisiae. besides, c. glabrata demonstrated the capability to grow in glucose levels as low as 0.01% in the spot dilution assay. in qrt-pcr analysis, differential expressions were observed in selected genes when c. glabrata was subjected to different glucose concentr...

Publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. By contrast, an enormous amount of expressed sequence tags (ESTs) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. Integrating protein an...

Chloroplasts are believed to be descendants of an ancestral endosymbiont related to cyanobacteria. Comparative genomics is expected to be useful in identifying the proteins that were transferred to chloroplasts from the endosymbiont. However, most of the present-day chloroplast proteins are encoded by the nuclear genome, and it was not until the nuclear genome of a land plant Arabidopsis thalia...

MOTIVATION Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies. RESULTS TopiaryExplorer supports the visualization of very large phylogenetic trees, including features such as the automated coloring of b...