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...

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...

this research was undertaken to evaluate and determine the risk of gas fluids and leakage of persian gulf star refinery on the environment in bandar abbas. through collection and compilation of research findings, we attempted to identify and work on factors leading to environmental risks. the risk factors were identified by hazop team and the risk score was calculated by multiplying the probabi...

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...

A consequence analysis was performed in one of the gas refineries in Iran to investigate the risks andpotential losses resulted from accidents. Specifically, the consequences of an explosion in LPGspherical tanks were modeled using PHAST and MATLAB software. In this paper, three methods ofcalculation of PHAST software TNT, multi-energy, and BST were used. The results showed th...

December 13, 2013 Copyright The code in src/pcre is Copyright (c) 1997-2010 University of Cambridge. All other code is Copyright (c) 2002-2010 University of California, Cornell University. Maintainer Melissa Hubisz License BSD_3_clause + file LICENSE Title R interface to PHAST software for comparative genomics Author Melissa Hubisz, Katherine Pollard, and Adam Siepel Desc...

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...