We present Meraculous2, an update to the Meraculous short-read assembler that includes (1) handling of allelic variation using " bubble " structures within the de Bruijn graph, (2) improved gap closing, and (3) an improved scaffolding algorithm that produces more complete assemblies without compromising scaffolding accuracy. The speed and bandwidth efficiency of the new parallel implementation ...

When applying a Genetic Algorithm to a new problem, how many generations should one reasonably expect to wait before reaching an acceptable solution? Using arguments based on information flow into the genepool, mediated by selection each generation, we present a rough and ready heuristic.

The island of Bali lies near the center of the southern chain of islands in the Indonesian archipelago, which served as a stepping-stone for early migrations of hunter-gatherers to Melanesia and Australia and for more recent migrations of Austronesian farmers from mainland Southeast Asia to the Pacific. Bali is the only Indonesian island with a population that currently practices the Hindu reli...

Common beans are a warm-season, food legume cultivated in areas prone to water limitation throughout their growing season. This study assessed the magnitude and pattern of trait associations for a total of 202 common bean genotypes divided into panels of 81 Andean and 121 Mesoamerican gene pool accessions grown under contrasting treatments of well-watered, non-stress, and water-limited, termina...

background: infections are readily transmitted as a result of bacterial contamination of swimming pools. therefore, hygiene and preventing the contamination of swimming pools is of particular importance. the objective of this study was to determine the amount of bacterial contamination in indoor pools of yazd in 2013. methods: in this descriptive and analytical study, all indoor swimming pools ...

BACKGROUND Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contribut...

We have generated a 3' cDNA pool from the RNA of only 1000 or fewer cells by reverse transcription (RT) from an extended oligo(dT) primer with a 3' degenerate base and a second strand primer with four degenerate 3' bases, followed by PCR. Reproducible differential displays (DD) can be made from this essentially inexhaustible source of DNA. The method produced DD patterns that are comparable but...

Selective inactivation of a target gene by antisense mechanisms is an important biological tool to delineate specific functions of the gene product. Approaches mediated by ribozymes and RNA-cleaving DNA enzymes (DNA enzymes) are more attractive because of their ability to catalytically cleave the target RNA. DNA enzymes have recently gained a lot of importance because they are short DNA molecul...

One goal of population genetics is to quantify and explain genetic structure within and among populations. Factors such as genetic drift, inbreeding, gene flow and selection are expected to influence levels and distribution of genetic variation. I review available data on genetic structure of vernal pool plant species with respect to these factors. Where relevant data are lacking, as is often t...

A software application called “Musical Gene Pool” is described. It was designed to evolve non-linear music from an initial random soup of sounds, which play continuously. Most evolutionary music systems to date require the user to select for musical aspects in a piecemeal fashion, whereas this system is experienced as continuous music throughout the entire process, as follows: a human listener ...