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PHASTER / PHAge Search Tool - Enhanced Release

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A significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. While 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 have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. PHASTER can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated GenBank file.

PHAST / PHAge Search Tool

A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. PHAST 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 and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage 'quality' and distinguish between intact and incomplete prophage. PHAST also produces extensive text summaries, downloadable figures, circular and linear genome views as well as colorful, zoomable, user-interactive graphics.

Phage Classification Tool Set

Obsolete
Provides a mechanism to determine the lifestyle of a phage. PHACTS is a web application which utilizes a similarity algorithm and a supervised Random Forest classifier to make a prediction whether the lifestyle of a phage, described by its proteome, is virulent or temperate. The software can determine the lifestyle of a phage using only genomic data and is able to distinguish between temperate phage proteins and virulent phage proteins even if they share similar functions.

PhageTerm

Analyzes DNA termini and phage packaging mechanisms using next-generation sequencing (NGS) data. The PhageTerm software works with sequencing reads in fastq format and the corresponding assembled phage genome. PhageTerm was validated on a set of phages with well-established packaging mechanisms representative of the termini diversity: 5’cos (lambda), 3’cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, it was used to determine the termini of 9 Clostridium difficile phages and 6 phages whose sequences where retrieved from the sequence read archive (SRA). This software is available as a standalone version for download. For direct graphical interface operation, a Galaxy wrapper version is also available.

PhiSpy

An algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies. PhiSpy is based on seven distinctive characteristics of prophages, i.e. protein length, transcription strand directionality, customized AT and GC skew, the abundance of unique phage words, phage insertion points and the similarity of phage proteins. The first five characteristics are capable of identifying prophages without any sequence similarity with known phage genes. PhiSpy locates prophages by ranking genomic regions enriched in distinctive phage traits, which leads to the successful prediction of 94% of prophages in 50 complete bacterial genomes with a 6% false-negative rate and a 0.66% false-positive rate.

VirSorter

Represents a scalable and community-available tool for detecting and identifying viral genome sequences from diverse microbial datasets. Its performance for prophage prediction is largely comparable to that of available prophage prediction tools when applied to complete microbial genomes, but it outperforms available tools when making predictions from modern microbial datasets which tend to be fragmented and larger-scale or when searching for viruses beyond those “known” in current databases. Thus, VirSorter complements existing tools to help elucidate bacterial and archaeal viral sequences among myriad modern microbial genomic data types. VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources.

Prophage Finder

Obsolete
Predicts prophage loci, based upon clusters of phage-related gene products encoded within DNA sequences. Prophage Finder provides results detailing several facets of these clusters to facilitate rapid prediction and analysis of prophage sequences. It was tested using previously annotated prokaryotic genomic sequences with manually curated prophage loci as benchmarks. Additional analyses from Prophage Finder searches of several draft prokaryotic genome sequences are also available.