Phages are viruses infecting prokaryotes. The sub-group of temperate phages has the capability to remain in their host, in a latent stage, as prophages. Most of the prophages are found integrated in the host chromosome while some are established as plasmids. Whether functional or defective, prophages can recombine with other phages and/or prophages, a central mechanism in bacteriophage evolution. Phophage detection software tools are used for identification and annotation of prophage sequences within bacterial genomes and plasmids.
Assists users to visualize, identify and annotate prophage sequences within bacterial genomes or plasmids. PHAge Search Tool performs identification using either raw or annotated bacterial genome sequence data. The main features are: (1) prophage region identification support for both raw nucleotide sequence input; (2) support for detailed prophage annotation including position, length, boundaries, number of genes, and attachment sites; and (3) support for the prediction of the completeness or potential viability of identified prophages.
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.
Combines similarity searches, statistical detection of phage-gene enriched regions and genomic context for prophage prediction. A database with prophage predictions in sequenced prokaryotic genomes has been developed with a web interface for browsing the results. Prophinder can also be accessed via a programmatic interface (web services), ensuring interoperability with other software tools.
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.
A heuristic computer program to identify prophage regions within bacterial genomes. Phage_Finder uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 searches against a collection of bacteriophage sequences and results from HMMSEARCH analysis of 441 phage-specific hidden Markov models (HMMs) to locate prophage regions. In addition to finding prophage regions, Phage_Finder has found integrated elements and integrated plasmids.
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.
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.