The PHylogenetic Analysis with Space/Time models (PHAST) software package consists of a collection of command-line programs and supporting libraries for comparative genomics. PHAST is best known as the engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser. However, it also includes several other tools for phylogenetic modeling and functional ele...

We present a ligand-based virtual screening technique (PhAST) for rapid hit and lead structure searching in large compound databases. Molecules are represented as strings encoding the distribution of pharmacophoric features on the molecular graph. In contrast to other text-based methods using SMILES strings, we introduce a new form of text representation that describes the pharmacophore of mole...

BACKGROUND The study is a continuation of a research carried out in Luweero district in Uganda1. It investigated whether PHAST was a suitable tool for reducing transmission of soil transmitted helminths. PHAST means Participatory Hygiene and Sanitation Transformation; a participatory approach that uses visual tools to stimulate the participation of people in promotion of improved hygiene and sa...

In English, gains in decoding skill do not map directly onto increases in word reading. However, beyond the Self-Teaching Hypothesis (Share, 1995), little is known about the transfer of decoding skills to word reading. In this study, we offer a new approach to testing specific decoding elements on transfer to word reading. To illustrate, we modeled word-reading gains among children with reading...

PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage 'cornerstone' feature identification steps to locate, annotate ...

PURPOSE To evaluate hearing aid handling skills for new and experienced users and to assess if such skills influence user's benefit and satisfaction. METHODS Seventy four participants (mean age of 70.43), experienced (n=37) or new hearing aid users (n=37) performed the tasks of "Practical Hearing Aid Skills Test" (PHAST), which were scored on a five-point Likert scale - higher scores indicate...

PHASTER (PHAge Search Tool - Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements ha...