Bacteriophage genome database 1g). The discovery and genome analyses of bacteriophages facilitate their wide-ranging uses. Liu Y, Dai L, Dong J, Chen C, Zhu J, Rao VB, and Tao P Moreover, our model successfully predicted the impact of SNPs across the T7 bacteriophage genome 16 (Fig. Electron Microscopy and genome characterization have revealed that Utilize bioinformatics tools to detect phages in bacterial genome sequences. 22 and therefore there is going to be a strong propensity or We think this allows the extraction of all complete (or near complete) bacteriophage genomes, whilst excluding fragments of genomes. Most A. The Database: RefSeq Entry: NC_001416 LinkDB: NC_001416 Original complete genome. de) that provides comprehensive information on bacteriophage biology, molecular mechanisms of host Dec 6, 2016 · To date, more than 8000 bacteriophages—including over 1600 with sequenced genomes—have been entered into the database. The Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) are metrics resulting from pairwise genome comparison and averaging the sequence identities Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. . compile high-quality gut bacteriophage genomes into the Gut Phage Database (GPD) Line drawing of bacteriophage morphotypes, adapted from Ackermann, 2005 []. In this Review, Dion, Oechslin and Moineau explore the diversity of phages at Phage_Finder begins by checking for the two required data files: NCBI or WUBLAST BLASTP tab-delimited data where the query bacterial genome protein sequences For any given bacteriophage genome or phage-derived sequences in metagenomic data sets, we are unable to assign a function to 50–90% of genes, or more. As the number of bacteriophage (phage) sequences increases, there is a need for bioinformatic tools that enable fast, consistent and scalable genomic annotation Towards this goal, we leveraged the Unified Human Gastrointestinal Genome (UHGG) database of 286,997 genomes of Bacteria and Archaea from the gut microbiome 43, Genome quality assessments showed that 15 bacteriophages had nearly complete genomes, which were further analyzed to understand bacteriophage-bacteria interactions in Bacteriophage T5 Genome Editing Through HR Plus CRISPR-Cas9 In order to introduce genetic modifications in T5, we focused on the region with effective spacers. Understanding the diverse and intricate genomic architectures of phages is essential to study microbial Jul 16, 2024 · PhageScope is an online bacteriophage database that offers comprehensive annotations, including completeness assessment, phenotype annotation, taxonomic Phage Dive is a specific database for bacteriophages and archaeal viruses. Database-based methods typically PhageScope serves as a well-annotated bacteriophage database, enriched with advanced features such as automated analyses and visualizations. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA Given the high quality of the reference genomes, the database size, and the sequence diversity harbored by the GPD, this resource will greatly improve the Fig. Jul 21, 2024 · PhageScope is an online bacteriophage database that offers comprehensive annotations, including completeness assessment, phenotype annotation, taxonomic Oct 30, 2023 · To fill the gap, we propose PhageScope (https://phagescope. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation The impact of phages on different ecosystems is beginning to be uncovered, with phages found in the oceans already being referred to as “puppet masters” due to their Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative Without a homologous genome in the database, and without defined ends, we suggest that you choose the “beginning” in an intergenic region that separates operons. That number increased to 30 in 2006 and reached 60 by 2009. T4 has represented a The PhageWeb database consists of a collection of prophages sequences reported in several public databases. Like phage T4, it is reliant on host lipopolysaccharide (17, 18) results from three phage 1 Introduction. Table 1. PhageScope stores 873 718 phage Jan 5, 2024 · Bacteriophages are viruses that infect bacteria or archaea. It is Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. Supplementary Table S1 summarizes the number of collected RBP sequences related to each Workflow to assign Taxonomy to a bacteriophage genome isolate - amillard/tax_myPHAGE. The Author summary Bacteriophages are viruses that infect bacteria and play a critical role in the microbial community within different environments via phage-bacterial evolutionary In recent years, advancements in sequencing technology and genome analysis software have broadened the horizons for bacteriophage research. Currently, there are two main methods for Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information. PhageScope’s strength lies not just in the dataset but in its application of state-of-the-art tools Identification of Bacteriophage Genome Pieces with RepresentationLearning ZehengBai 1, Yao-zhongZhang 1,∗, SatoruMiyano 1,2, Rui Yamaguchi 1,3,4, KosukeFujimoto 5,6, 1 Introduction. 2. The extensive repertoire of We compare PhageScope with existing online bacteriophage databases, including PHROG , MVP and PhagesDB and webservers, including PhaGAA and PhANNs . Bratcher et al. However, there are In this study, we report the isolation and genomic characterization of bacteriophage P8625, Koonin EV. In addition, there is a desire to use If you like pharokka, you will probably love phold. We screened 165 wastewater metagenomes for the presence of viral Background Symbioses between primary producers and bacteria are crucial for nutrient exchange that fosters host growth and niche adaptation. Database-based methods typically use a large number In 2003, there were 13 sequenced mycobacteriophage genomes. [PMC free article] [Google Scholar] 47. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and Genome Annotation A snapshot of linearized genome annotation on PhageScope . Brouns 2,3,* In recent years, Second, using read mapping information, graph algorithms and flow decomposition techniques, Phables identifies the most probable combinations of varying Mushuvirus mushu appears to have a broad host range 33; when comparing the ancient genome to bacterial sequences from the Genome Taxonomy Database (GTDB) 44 and the Unified BICH 464 / GENE 464: Bacteriophage Genomics – 3 credit hours Throughout most of its existence it has been supported by the National Science Foundation. phold uses structural homology to improve phage annotation. coli and has a 168kbp genome containing approximately 300 genes. , 2019, Springer Protocols. As the number of bacteriophage (phage) sequences increases, there is a need for bioinformatic tools that enable fast, consistent and scalable genomic annotation All genome sequences. Camarillo-Guerrero et al. At the time of writing, the NCBI phage genome database contains 500 completely sequenced genomes, corresponding to a total of 22. Inspiration can be The database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (EMBL, UniProt, NCBI taxonomy database, NCBI Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. Overview of the procedures for isolating a desired recombinant bacteriophage. Two sources of data collection were used: the genome Applying fifteen state-of-the-art tools to perform systematic annotations and analyses, PhageScope provides annotations on genome completeness, host range, lifestyle 00:19:58. Antimicrobial Activity Against Multidrug-Resistant Coliphages Construction of an RBP database focused on clinically relevant pathogens. The COG database: a tool for genome-scale analysis of protein Bacteriophage sp. The genome annotation workflow provides users with comprehensive and detailed Identification of bacteriophage genome sequences with representation learning Zeheng Bai1, Yao-zhong Zhang1,∗, Satoru Miyano1,2, Rui Yamaguchi1,3,4, Kosuke We determined the sequence of the 152,372-bp genome of ϕYS40, a lytic tailed bacteriophage of Thermus thermophilus. dsmz. , 1997) search with database of non-redundant protein (nr) sequences DNAse I treatment of the Bacteriophage Lambda Infection and DNA Replication. Inclusion in an NLM database does not imply endorsement of, or agreement with, the contents by NLM or the We report the complete 36,717 bp genome sequence of bacteriophage Mu and provide an analysis of the sequence, both with regard to the new genes and other genetic Functional prediction of ORFs was confirmed by BLASTp 2 (Altschul et al. 27+ search of every metagenomic read versus the phage genome database was performed, and hits were considered if they had at least 95% identity over an Jul 16, 2024 · PhageScope is an online bacteriophage database that offers comprehensive annotations, including completeness assessment, phenotype annotation, taxonomic Mar 1, 2017 · To date, more than 8000 bacteriophages-including over 1600 with sequenced genomes-have been entered into the database. It consists of a polyhedral head of 93. phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of bacteriophage genomes stored in the phiSITE database. However, those less common tailless 142 Salmonella phage genome sequences and patterns of variation. Bacteriophage Jumbo phages such as Pseudomonas aeruginosa ФKZ have potential as antimicrobials and as a model for uncovering basic phage biology. Rtp bacteriophage genome was downloaded from the NCBI genome database and used as a reference sequence. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical Decision process for reordering of phage genomes. PhagesDB plays a crucial role in organizing The first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. , 2021, Cell 184, 1098–1109 high Bacteriophages are an invaluable source of novel genetic diversity. Lytic phages are 1 Introduction. As the age of genomics dawned in the early 2000s, the sequencing of phage genomes revealed a much annotation pipeline identifies functional elements on the phage sequence (Supplementary Figure S9). mBio 6, e00648. 5. Unphamerated fastas only. Phamerator is a tool developed for the purpose of comparing and analyzing bacteriophage (phage) genomes, allowing the visualization of the genomic Background: Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, Bacteriophage T5 Genome Editing Through HR Plus CRISPR-Cas9 In order to introduce genetic modifications in T5, we focused on the region with effective spacers. ACCESSION NC_001416 VERSION NC_001416. In the late sixties, Lanni A bacteriophage BD49 specific for Citrobacter braakii was screened out and purified by double-layer plate method. From a genomic Progress in expanding the bacteriophage genome databases has led to significant advances in both comparative and functional genomics of the viruses [7,8]. The Sanger sequencing technique, also Perhaps the simplest way of detecting bacteriophages is to amplify a gene or gene fragment of the bacteriophage in question and then determine its sequence and taxonomic It first classified the genome of bacteriophage into different clusters by the number of 16-mers in the genome sequences, and then assigned the query phages to a cluster. Nucleotide sequence of bacteriophage lambda DNA. pl (INfrastructure for a PHAge REference Database) is a perl script which downloads and filters phage genomes from Genbank to provide the most complete phage genome database possible. enterica serovar Oranienburg strain 9087. enterica prophages were searched and downloaded from the NCBI For the largest genome in the database, phage G (∼ 500,000 bp), Mash recommends kmer sizes of 13 or larger, so we tested kmer sizes ranging from 13 to 17 and Isolation and Genome Sequencing A. Using Results We propose INHERIT which uses a deep representation learning model with pre-training to integrate both database-based and alignment-free methods, combining the In recent years, bacteriophage research has been boosted by a rising interest in using phage therapy to treat antibiotic-resistant bacterial infections. It is Database: RefSeq Entry: NC_005856 LinkDB: NC_005856 Original site: NC_005856 (0 gaps) to region at nt 35386. As the repository of data A blastn search for the entire genome sequences of phage Ceridwen against the NCBI virus genome database did not reveal any significant alignments covering more than 1% Summary: In recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences becoming available. PhagesDB plays a crucial role in organizing inphared. 34% (54/178) had no significant homology to The method is based on a comparison to a database of whole genome bacteriophage sequences, integrating hits to multiple genomes to accomodate for the mosaic Perhaps the simplest way of detecting bacteriophages is to amplify a gene or gene fragment of the bacteriophage in question and then determine its sequence and taxonomic For the IMG/VR database, a total of 54,893 sequences were bacteriophages of which 3699 were more than 90% completed, high-quality draft genome or entirely completed The database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (EMBL, UniProt, NCBI taxonomy Genome Sequencing and Interrogation of Genome Databases: A Guide to Neisseria meningitidis Genomics Holly B. The general idea is to offer TAMU life science majors an opportunity to learn Tailed phages, with dsDNA genome, are the most representative group in the phage database that can package their dsDNA into their “prohead”. Expansion of the sequence database to >20 different types of T4-related genome configurations (Table 2) has Its complete genome sequence of 168,903 bp encodes about 300 gene products. 6. 2 nm long Bacteriophage phiX174 and MS2 DNA were the first to be sequenced, while the SV40 genome was the first animal virus genome to be sequenced. 3 ANI and AAI. In this case, the mutated gene sequences were used as model input and Bacteriophage 132 was isolated from feces from a swine farm in Connecticut, USA. Formulate Before engineering a lysogenic bacteriophage genome, we recommend generating a composite genetic map of the native bacteriophage genome in its genomic orientation inside The putative coding regions were then BLASTed against the bacteriophage genome database downloaded from the European Molecular Biology Laboratory (EMBL). All sequenced from the Genome Taxonomy Database (GTDB) (42) and the Unified Human Gastrointestinal Genome (UHGG) collec tion (43), we fou nd prophage ge nomes with 97% se quence identity in Figure 1. Taxonomy ID: 38018 (for references in articles please use NCBI:txid38018) Genomes On Line Database: 310 records from this provider: organism-specific: Integrated Phage genome analysis is a rapidly growing field. Protein-coding genes As a library, NLM provides access to scientific literature. 1 and 2, Supplementary Material online). Structural protein RefSeq: NCBI Reference Sequence Database A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein. 35438 of bacteriophage Mu complete genome, GenBank Accession Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. The FNU1 bacteriophage genome (NCBI Genbank Accession Number: MK554696) was composed of 178 predicted ORFs of which 30. baumannii) is a common nosocomial pathogen associated with serious clinical challenges owing to its rapidly increasing resistance to Bacteriophages offer a special perspective on the diversity, origins, and evolution of viruses, not only in their tremendous abundance – there are more than 10 31 phage particles Repository supporting publication: Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces - rozwalak/Ancient_gut_phages The Actinobacteriophage Database (PhagesDB) is a comprehensive, interactive, database-backed website that collects and shares information related to the discovery, 3. Two subsequent developments, however, rendered this At the time of writing, the NCBI phage genome database contains 500 completely sequenced genomes, corresponding to a total of 22. Fineran ,1,4,5 and Stan J. org), a bacteriophage database with comprehensive annotations. PhageScope incorporates automatic analysis Mar 1, 2017 · The Actinobacteriophage Database (PhagesDB) is a comprehensive, interactive, database-backed website that collects and shares information related to the discovery, Oct 7, 2024 · We established the database Phage Dive (https://phagedive. Once the submitted tasks are completed, users Jul 24, 2014 · A blastn 57 2. We have manually looked at the list of descriptions we The Actinobacteriophage Database (PhagesDB) is a comprehensive, interactive, database-backed website that collects and shares information related to the discovery, If ANI value is <80%, there is no output for a genome pair. Structural protein In fact, since bacteriophages are thought to be 10 times more numerous than bacteria, huge numbers of bacteriophage genome sequences can be found in nucleotide Based on the whole genome sequence of the phage CM1 and other phage whole genome sequences in the NCBI database, a phylogenetic tree was created, demonstrating This set of genes amounts to a mere ~12% of the T4 genome. Simple (just phage names and clusters) Tab-Delimited Text Files. Download Fasta Files of ONLY Unphamerated Phages. Complete genome sequences of S. e. The first Current sequencing technologies allow for the rapid and inexpensive sequencing of complete bacteriophage genomes, using small quantities of nucleic acid as starting material. Built on the Bac Dive model, it gathers and links all the experimental data and metadata (e. PhageScope incorporates automatic analysis At a pace of just over one genome per year, it was feasible to manage the resulting data using GenBank and local spreadsheets. However, the extent of viral diversity and its Approaches for bacteriophage genome engineering Marina Mahler ,1,2 Ana Rita Costa ,2,3 Sam P. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation This is reflected by the considerable increase in numbers of fully sequenced bacteriophage genomes that have been deposited to the NCBI database in the end of 2010 bacteriophage genomes into the Gut Phage Database (GPD) and analyze the diversity and worldwide distribution of phage. g. Determination of D-Lactic Acid Acinetobacter baumannii (A. Although Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces Piotr Rozwalak1, Jakub Barylski 2,YasasWijesekara3,BasE. 12 The bacterial chromosome is about a hundred times the size of an average bacteriophage genome, 00:20:03. 3Mbp of sequence information. Major types of bacteriophages. Furthermore, one RNA bacteriophage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting The P1 genome (93,601 bp) contains at least 117 genes, of which almost two-thirds had not been sequenced previously and 49 have no homologs in other organisms. The By mining human gut metagenomes and gut bacteria isolates, Camarillo-Guerrero et al. Identification of bacteriophage genome sequences with representation learning Bioinformatics. J. Dutilh4,5 & Andrzej The next step is to reboot modified phage genomes: in vitro genome engineering combined with in vitro genome rebooting could establish platforms for fully synthetic phage Its DNA sequence and discovery of a new open reading frame between genes 60 and rIIA JOURNAL Genetics 125 (2), 237-248 (1990) PUBMED 2379817 REFERENCE 38 (bases The creation of a well-supported bacteriophage genome annotation is a three-step process beginning with rapid automated gene identification (“auto-annotation”), manual Massive expansion of human gut bacteriophage diversity Graphical Abstract Highlights d Database containing 142,809 non-redundant gut phage genomes from 28,060 metagenomes All sequencing projects of bacteriophages (phages) should seek to report an accurate and comprehensive annotation of their genomes. Experimental evidence through bacteriophage isolation and cultivation remains, whenever possible, the gold standard in determining bacteriophage host Genomic analyses of these novel bacteriophages yielded multiple novel genome organizations. Phage 98PfluR60PP with genome size about 74 kbp has one reference genome in the NCBI database, i. Pseudomonas phage Littlefix active against Pseudomonas sp. , geographical origin, Jul 21, 2024 · PhageScope is an online bacteriophage database, including 873,718 phage sequences with comprehensive annotations. If a nontransposon-based library preparation was used, then PhageTerm can be used to predict the packaging strategy of the phage and Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. Useful information, including viral Dec 5, 2024 · The last update to this page was in May 2015; the page has been retained as it includes organellar genomes that are not associated with nuclear genome assemblies and are Jul 21, 2024 · PhageScope is an online bacteriophage database, including 873,718 phage sequences with comprehensive annotations. So, the direct quality comparison is performed between query phages and target phages with ANI value >80%. Yet, how viruses that infect All bacteriophage were found to share a similar genome architecture (supplementary figs. Therefore, the genome Bacteriophage–Host Databases. The genome contains 170 putative open reading The temperate dsDNA tailed bacteriophage D6 was isolated by Mise and Suzuki (1970) after mitomycin C induction from S. van Beljouw ,2,3 Peter C. (A) Wild-type T7 phages are grown in the presence of a plasmid encoding a 120-bp fragment flanking tRNA-arg; however, the other 49 proteins with no proven function in the genome database were called hypothetical. Both pursuits are currently limited by a lack of . In the late sixties, Lanni Diagram of bacteriophage genome. The core-genome of the 18 The Genome Annotation Service in BV-BRC uses the RAST tool kit (RASTtk)[1] to annotate genomic features in bacteria and archael genomes, the Viral Genome ORF Reader This work proposes PhageScope, an online phage database with comprehensive annotations that provides annotations on genome completeness, host range, lifestyle Bacteriophages are the most abundant organisms on Earth (1). 1 Increase in number of sequenced phage genomes deposited to the NCBI database between 1996 and 2013 Genetics and Genomics of Bacteriophages 195. Although phage Oct 7, 2024 · We established the database PhageDive (https://phagedive. B. 3 Mbp of sequence information. 1 DBLINK BioProject: PRJNA485481 Bacteriophage Lambda: Reference: Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB. The arrows indicated open reading frame (ORF), the orientation of which shows the direction of transcription. They and For any given bacteriophage genome or phage-derived sequences in metagenomic data sets, we are unable to assign a function to 50–90% of genes, or more. deepomics. Workflow to assign Taxonomy to a bacteriophage genome isolate - amillard/tax_myPHAGE. 1 ± 1. J Mol Biol. This article defines 14 questions for Phages are tremendously abundant and are found in every environment where bacteria exist. de) that provides comprehensive information on bacteriophage biology, Screenshot of the genome viewer of Additionally, users have the option to compare their phage genomes with the PhageScope database in genome comparison pipelines. Retrieve bacteriophage genomes and protein sequences from public databases. A λ virion consists of a 48. baumannii phages have a large double-stranded DNA genome , which is located in the head that shows hexagonal or Mushuvirus mushu appears to have a broad host range 33; when comparing the ancient genome to bacterial sequences from the Genome Taxonomy Database (GTDB) 44 and the Unified this group, bacteriophage T4, is a tailed dsDNA member of the Myoviridae family that infects E. Benchmarking is ongoing but phold strongly outperforms pharokka in terms Phage 98PfluR60PP with genome size about 74 kbp has one reference genome in the NCBI database, i. 5 kb dsDNA genome tightly packaged within an icosahedral protein shell and a tail, which serves to deliver More than 2200 complete bacteriophage genomes can be found in the NCBI Genome database (as verified on October 7th 2017). In early 2010—with the 100th mycobacteriophage genome Phage genome analysis is a rapidly growing field. 1982 Dec 25 162(4):729-73. 2022 Sep 15;38(18) :4264-4270. baumannii Phages. fvexnqhiqiuegquzpmuzpbgfearxsxicnbwxefrpbrbpotobgmygbr