Bacteriophage genome database
Bacteriophage genome database
Bacteriophage genome database. Single-read versus paired-end sequencing Mar 23, 2005 · Based on their genome size, organization of their gene map and comparative nucleotide and protein sequence analysis, the S. In many genome-sequencing projects, the presence of integrated genomes of temperate May 3, 2023 · The isolated bacteriophage was purified and amplified, followed by testing of its molecular weight using Pulse-Field Gel Electrophoresis (PFGE), transmission electron microscopy, antibacterial activity against a panel of other Klebsiella pneumoniae hosts, stability studies, and whole genome sequencing. A total of 11914 phage genome accession numbers were downloaded from their website Apr 30, 2023 · Acinetobacter baumannii (A. Aug 3, 2022 · Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. nucleatum bacteriophage genome in the database is the prophage ΦFunu1, which is phylogenetically distant from FNU1, sharing very little genetic homology. The extensive repertoire of phages, coupled with the comprehensive genome annotations and sequence comparison results from systematic analyses assisted with fifteen state-of-the-art tools, provide details Jul 10, 2017 · 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 sketch values of 200, 1,000, 5,000 Mar 1, 2017 · 3 Features. So, the direct quality comparison is performed between query phages and target phages with ANI value >80%. Dec 1, 2022 · Functional assignment of predicted CDS is conducted using the PHROGs database (Terzian et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator Sep 26, 2022 · Bacteriophages, also known as phages, are viruses that infect and replicate only in bacterial cells. For example, for two phage isolates to be considered members of the same bacteriophage species, their nucleotide sequences must be at least 95% identical across the length of their entire genomes in a pairwise comparison (percent identity × query coverage). baumannii phages have a large double-stranded DNA genome , which is located in the head that shows hexagonal or pentagonal outlines with icosahedral symmetry. (2010) [5] . Phages Arawn and Idris. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Throughout most of its existence it has been supported by the National Science Foundation. baumannii Phages. In the present study, we isolated and characterized a new Siphoviridae phage, named “Pseudomonas phage vB_PsyS The developmental pathways of many double-stranded DNA (dsDNA) viruses, both prokaryotic and eukaryotic, are remarkably similar. 5%. PhageScope incorporates automatic analysis and interactive visualization. May 15, 2024 · The entrance of a phage into a bacterial genome is performed through the process of lysogeny, forming a “dormant” prophage containing the entirety of the bacteriophage DNA that is not actively Jan 31, 2021 · 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 affiliation, a method called amplicon sequencing. Moreover, Phables has recovered the circular genome of Enterobacteria phage P22 and the linear genome of Enterobacteria phage T7 as well. The tail can adsorb to bacteria and varies in length. The general idea is to offer TAMU life science majors an opportunity to learn about modern genomics by real hands-on research experience in which they annotate a new phage genome. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA phage genome sequences are available from the NCBI Genome database (June 2019). Database-based methods typically use a large number of sequences as references; alignment-free methods usually learn the features of the sequences with machine learning and deep learning models. Oct 1, 2011 · Nucleotide sequence comparison of bacteriophage genomes reveals them to be enormously diverse [1]. SPP1 belongs to the Siphoviridae family. Its complete genome sequence of 168,903 bp encodes about 300 gene products. 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 not represented in the above search. A separate daily cronjob checks whether there’s a new version of the Actino_Draft Phamerator database, and if so it accordingly updates the local Pham information and blastp database. Dec 16, 2021 · All sequencing projects of bacteriophages (phages) should seek to report an accurate and comprehensive annotation of their genomes. aureus phages can be organized into three groups. These pages contain detailed information about the phages, including discovery details (GPS coordinates, year found, isolation temperature, host bacterium, etc. It lysogenizes its hosts as a circular, low-copy-number plasmid. For example, unless any given phage genome has a known close relative that infects the same host, or there is a closely-related prophage, it is unusual to find extensive nucleotide sequence similarity to other database entries. PhageScope is an online bacteriophage database, including 873,718 phage sequences with comprehensive annotations. 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 aligned length of 75 bp Jan 15, 2021 · 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 genomes (the latter Size distribution of sequenced bacteriophage genomes. Its genome length and content are similar to that of other phages in the Actinobacteriophage Database BC cluster. The numbers of sequenced genomes in each size range is shown. Feb 1, 2018 · The temperate Escherichia coli bacteriophage D6 can exist as a circular plasmid prophage, and we report here its 91,159 bp complete genome sequence. Each box represents a single open reading frame; conserved genes shown in grey, and Nov 1, 2011 · phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of bacteriophage genomes stored in the phiSITE database. Alignment of the phage genomes shows that these phages are closely related. uk/ena/data/warehouse/search?portal=assembly. ac. Jan 23, 2018 · Welcome to the Actinobacteriophage Database at PhagesDB. In total, 13,429 (9. Jan 27, 2024 · Complete genome analysis revealed that the phage Kp109 has a long linear double-stranded (ds) DNA genome with length and average GC content of 51,630 bp and 51. To date it contains detailed information about more than 700 experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from 32 bacteriophages belonging to Siphoviridae, … Bacteriophages occupy a unique position in biology, representing an absolute majority of all organisms in the biosphere. “Unverified,” “partial” or “incomplete” phage genomes were excluded. File is called all_PHROGs. In these cases, alignment-free methods offer a promising alternative to infer bacteriophage–host relationships by studying the similarity in patterns of sequence composition, such as codon usage or oligonucleotide (short nucleotide fragment) frequency []. 1 < τ < 0. We have determined the complete nucleotide sequences of two strains of a P1 thermoinducible mutant, P1 c1-100. However, the existing phage databases are short of meticulous annotations. Aug 24, 2021 · Rtp bacteriophage genome was downloaded from the NCBI genome database and used as a reference sequence. 13-2/db/hmm/ to use with prokka Contained within this repository are worked examples for the assembly and annotation of a bacteriophage genome. Most A. , geographical origin, isolation source) of the viruses present in different culture collections (Laval collection, NCTC, DSMZ). Oct 1, 2011 · Nucleotide sequence comparison of bacteriophage genomes reveals them to be enormously diverse . pylori phages have a pan-genome consisting of 75 genes and a soft-core genome of 10 genes, which includes genes involved in the lytic and lysogenic life cycles. Viral and host sequences may lack sequence homology, making them less well-suited for alignment-based methods. [1][2][3] However, all consist of a nucleic acid genome encased in a shell of phage-encoded capsid proteins, which Aug 25, 2021 · Bacteriophages are an invaluable source of novel genetic diversity. These span at least 70 different bacterial hosts, with two-thirds of the sequenced genomes of phages representing only eight bacterial hosts. 5. Annotations predict 73 coding features, including four tRNAs (Pro, Tyr, Asp, and Asn). PhageScope incorporates automatic analysis and interactive visualization for both curated and customized data. To date, genetic knowledge regarding L. Jul 18, 2022 · The complete circularly permuted genome of PaCe is 45,365 kb in length, with a GC content of 52. Reference: How to cite this resource - Schoch CL, et al. Full genome sequences were available for 142 phages (Document S1) and their corresponding genomic information are summarized in Table S1 and include accession number, phage name, assigned cluster, host species, genome size Dec 20, 2021 · Genome of BI-EHEC was successfully annotated using multiPhATE2. Aug 26, 2016 · Results. Aug 20, 2022 · Phage P1 was isolated from the abnormal fermented liquid using Lactobacillus plantarum (L. Complete genome sequences of S. 12 The bacterial chromosome is about a hundred times the size of an average bacteriophage genome, 00:20:03. Jan 5, 2024 · Bacteriophages are viruses that infect bacteria or archaea. Antimicrobial Activity Against Multidrug-Resistant Coliphages The prevalence of antibiotic resistance (AMP, TCN, and Colistin) and extended-spectrum beta-lactamase (ESBL) production has considerably escalated in all terrestrial regions. Comparison of their gene maps reveals extensive genome mosaicism, hinting to a large reservoir of unidentified S. tar. Due to their high host specificity and easy access to the natural environment, bacteriophages (phages) may serve as good antibacterial agents. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank Nov 16, 2023 · As indicated above, the ICTV has added nucleotide sequence homology as a primary component of the viral classification system []. baumannii) is a common nosocomial pathogen associated with serious clinical challenges owing to its rapidly increasing resistance to antibiotics. For example, unless any given phage genome has a known close relative that infects the same host, or there is a closely related prophage, it is unusual to find extensive nucleotide sequence similarity to other database entries. This genetic material is packaged into a capsid that can be polyhedral (Microviridae Jan 14, 2021 · The third source of raw data collection was the phage genome database constructed by Millard and colleagues. The genome has a length of 43,100 bp and contains 68 predicted protein-coding genes and no tRNA genes. 1C). However, new users attempting bacteriophage analysis can struggle to select the best methods and interpret the variety of results produced. Apr 30, 2023 · Isolation and Genome Sequencing A. 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. DNA Master *. Variations on … Dec 9, 2023 · For each genome pair, these values are given at the intersection of the corresponding row with the corresponding column, as follows (from the top to bottom of the intersection square): (i) aligned fraction genome 1, representing the proportion of the genome found on the row that has been aligned to its pair (the genome on the column); (ii Jun 24, 2019 · The only F. Consequently, there is a need for a rapid and consistent genomic annotation tool dedicated for bacteriophages. Determination of the location and function of the gene features within the genome sequence, or annotation, is a necessary nex … Sep 9, 2022 · Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. Even more recent than the discovery of phage-encoded CRISPR-Cas systems, anti-CRISPR genes are also a topic of current research. Concurrently, viral gene Sep 29, 2016 · 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 genome structure of many bacteriophages. SPP1 is a virulent double-stranded DNA (dsDNA) phage that infects the Gram-positive bacterium Bacillus subtilis strain 168. . The original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. 96% ANI). Bacteriophage P8625 was selected for genome sequencing because of its importance to understand bacteriophages infecting members of the Verrucomicrobia that are known to play crucial ecological roles in the ocean . Bacteriophages can have different packaging strategies that will result in different genomic termini or circularly permuted genomes. Because their genomes are relatively small, elucidating the genetic diversity of the phage population, deciphering their origins, and identifying the evolutionary mechanisms that … Apr 4, 2020 · The GenBank database contains over 2580 complete genome sequences from bacteriophages. coli and has a 168kbp genome containing approximately 300 genes. The genome lacks known lysogeny genes using a set of HMMs, suggesting that PaCe has a strictly lytic lifestyle . Phage therapy has been successfully used to treat antibiotic-resistant A Jan 1, 2024 · PhageScope serves as a well-annotated bacteriophage database, enriched with advanced features such as automated analyses and visualizations. Up-to-date assembly data are searchable from https://www. Feb 23, 2024 · Here, we present bacteriophage SoJo, a siphovirus infecting Streptomyces mirabilis, with a circularly permuted genome of 39 kbp and GC content of 71. Oct 12, 2011 · Background Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation. The virion is composed of an icosahedral, isometric capsid (∼60 nm diameter) and a long, flexible, noncontractile tail. We have manually looked at the list of descriptions we extract to identify obvious fragments eg 21 kb region of a cyanophage genome. Sep 7, 2022 · To date, a variety of bacteriophage identification tools have been developed that differ in the phage mining strategies used, input files requested, and results produced. Integrases induce homologous DNA recombination between the two sites to either integrate the phage genome into the bacterial genome or (with the help of an RDF or excise) remove the prophage from the bacterial genome. org, an interactive site that collects and shares information related to the discovery, characterization, and genomics of phages that infect bacterial hosts within the phylum Actinobacteria. 5% and a coding density of 89. Oct 14, 2021 · We report the discovery and genome sequence of phage Adumb2043, a siphovirus infecting Arthrobacter globiformis, B2979-SEA. Oct 28, 2010 · An overview of how the sequenced T4-like Viruses differ from each other. 22 and therefore there is going to be a strong propensity or at least an opportunity 00:20:08. Sep 29, 2021 · For reconstruction of evolutionary history, complete genome sequences resulting from BLAST search and well-annotated reference sequences (RefSeq database 74) were retrieved from the NCBI Virus P1 is a bacteriophage of Escherichia coli and other enteric bacteria. Database containing 142,809 non-redundant gut phage genomes from 28,060 metagenomes Jul 24, 2014 · A blastn 57 2. Jun 17, 2023 · Conserved and accessory gene map. Quantitative analysis of recombination events of the soft-core genes showed Jan 1, 2024 · PhageScope serves as a well-annotated bacteriophage database, enriched with advanced features such as automated analyses and visualizations. Jun 24, 2019 · The only F. , 2021; Fig. Aug 24, 2021 · The genome of phage MSK was sequenced, comprising 45,053 bp with 44. 6%) as high quality, and 101,381 (70. Nov 16, 2018 · 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 affiliation, a method called amplicon sequencing. Among the phages in the largest size 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. Phage Dive is a specific database for bacteriophages and archaeal viruses. Structural and lytic cycle-related proteins such as head, tail, capsid, and lysozyme (lysin) were annotated. 3 kbp to 316 kbp. Size intervals are 5 kbp from 2−100 kbp, and 25 kbp from 100−300 kbp. Alignment-Free Methods. Moreover, a database of Cas genes can be used to search for Cas genes in bacteriophage genomes [62, 63]. Mar 18, 2021 · Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we analyse draft and complete genomes assembled from 150–5300 years old palaeofaeces and human gut-content samples17,19–23. Bacteriophage naming and taxonomy Newly isolated bacteriophages were named according to rules and conventions in the field and classified in line with the rules of the International Committee on Oct 4, 2016 · Although 1,910 complete bacteriophage genome sequences (and 77 genomes of viruses infecting archaea) have been deposited at the NCBI database, this number is low compared to 67,806 complete genome Bacteriophage Genomics has actually been in operation for over 20 years now. 00:19:58. Aug 26, 2016 · Background Phage genome analysis is a rapidly growing field. Nov 9, 2017 · Before deciding that a newly sequenced bacteriophage genome fits within an existing or new genus one should review all the evidence: host, morphotype, life style, genome characteristics (kb, mol% G + C, number of CDS, tRNAs), DNA–DNA relatedness, % protein homologs, and phylogeny. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Oct 30, 2023 · This work proposes PhageScope, an online phage database with comprehensive annotations that provides annotations on genome completeness, host range, lifestyle information, taxonomy classification, nine types of structural and functional genetic elements, and three types of comparative genomic studies for curated phages. A cumulative GC Skew of the phage genome was generated for the identification of the location of origin of replication and terminus point. Mar 6, 2023 · If ANI value is <80%, there is no output for a genome pair. 05 for the phage genome to recombine with the bacterial chromosome. Mar 21, 2013 · In addition to more than 1700 bacteriophage genomes, the above described advances in DNA sequencing technologies have enabled the generation of more than 3500 complete and 11 000 incomplete bacterial genome sequences (Gold genomes database, November 2012). In total, 73 open reading frames (ORFs) were predicted, out of which 24 showed a close homology with known functional proteins, including one tRNA-arg; however, the other 49 proteins with no proven function in the genome database were called hypothetical. Here, we investigated the whole genome sequence of L. 8% G + C composition. T4 has represented a model for bacteriophage genetics over the past 80 years, upon which important fundamental phage structural and phenotypic characteristics have Aug 15, 2017 · The number of phage genome copies per concatemer (C) reported in the literature is typically smaller than 10 19 and therefore 0. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae , Podoviridae, and Siphoviridae . Jul 13, 2020 · A blastn search for the entire genome sequences of phage Arian and Bo-Finn against the NCBI virus genome database did not reveal any significant alignments covering more than 8% of the query genome. The phylogenetic tree of tail fiber protein and BRIG results showed that BI-EHEC was similar to phages of the same host in the bacteriophage genome database. Integrase A recombinase that binds to the AttP and AttB sites between the phage genome and host genome, or AttL and AttR sites in a lysogen. After reviewing all the data you may decide to lump or split. Before any genome assembly, it is important to determine in advance what is required from the final genome assembly. They are extremely diverse in size, morphology, and genomic organization. We think this allows the extraction of all complete (or near complete) bacteriophage genomes, whilst excluding fragments of genomes. enterica prophages were searched and downloaded from the NCBI database. The P1 genome (93,601 bp) contains at least 117 genes, … The gene-level analysis showed that, after parameter tuning of the prokaryote pan-genome analysis program, H. ), sequencing details (genome length, G + C content, type of genome termini, etc. The target phages are provided from the self-construct phage genome database (15 709 whole phage genomes download from NCBI). The first publically accessible version of the phiSITE genome browser was described by Klucar et al. The Actinobacteriophage Database at PhagesDB. SoJo was isolated from soil in Columbia, MD, USA. 1 The phage head encloses the mature SPP1 chromosome, which is a linear double-stranded DNA molecule of ∼45. Sep 21, 2023 · The slightly low genome coverage for Staphylococcus phage SAP2 TA-2022 may have been due to the omission of the dead-end which was not properly assembled. However, limited reports are available concerning phages can that lyse members of Pseudomonas syringae, although this is a widespread bacterial species that can infect almost 200 plant species. 64%, respectively. This can be straightforward if the target bacteriophage has a published genome in an INSDC database. Oct 30, 2023 · Bacteriophages are viruses that infect bacteria or archaea. 2. Oct 1, 2008 · The past three years have seen an escalation in the number of sequenced bacteriophage genomes with more than 500 now in the NCBI phage database, representing a more than threefold increase since 2005. 99%) as genome fragments (<90% complete). this group, bacteriophage T4, is a tailed dsDNA member of the Myoviridae family that infects E. With further rules to exclude these specific fragments. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. The T4-related genomes sequenced so far exhibit divergence from one another in several respects including; (a) the range of bacterial host species that the respective phages infect, (b) the sizes of these genomes and the capsids (phage heads) in which they are packaged, (c) the types of modifications, if any, that the Nov 17, 2022 · Thus, the analysis resulted in the finding of 16 different genome organizations at the putative lysis cassette that encompassed a total of 77 phages. Dec 6, 2016 · In order to ensure that recently-sequenced genomes appear promptly in local blast results, a cronjob updates the local blastn database three times a week. … Jan 23, 2024 · 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 Human Gastrointestinal The first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. The PHROGs database contains 38 880 PHROGs (protein orthologous groups) containing 868 340 proteins from 17 473 complete genomes of viruses infecting bacteria or archaea that are grouped together using remote homology detection. 2010 organisms. ), characterization details May 26, 2020 · 142 Salmonella phage genome sequences and patterns of variation. Dec 16, 2021 · Presequencing. They are ubiquitous in the environment and recognized as the earth's most abundant biological agent. Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. plantarum phage diversity is still limited, and further in-depth sequencing analysis of isolated L. We have developed phiSITE, database of gene regulation in bacteriophages. Butyrivibrio phages Arawn and Idris also share high sequence similarity (98. Adumb2043 was isolated from soil collected in Colorado Springs, Colorado. Jun 24, 2021 · 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, which represents 4,644 prokaryotic Nov 5, 2021 · All annotations are maintained from the PHROGs database set. plantarum phage P1, sequenced by Illumina HiSeq Jan 31, 2021 · To this end, the recent development of a technique known as “bacteriophage recombineering of electroporated DNA (BRED)” has provided a novel approach to bacteriophage genome modification by using phage-encoded recombination systems in order to engineer deletions, point mutations, and small insertions into a desired location (Marinelli et al Jan 12, 2022 · 2. 6%. aureus phage genes. plantarum) IMAU10120. Results We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of In recent years, bacteriophage research has been boosted by a rising interest in using phage therapy to treat antibiotic-resistant bacterial infections. Apr 3, 2017 · The availability of genome sequence data also gave rise to a range of potential classification or grouping schemes, such as the Phage Proteomic Tree [], phage network clusters [], kmer-based grouping [], signature genes-based grouping [], or whole genome nucleotide identity-based grouping [], which were not always compatible with the rules laid out in the ICTV Code and/or the International Current sequencing technologies allow for the rapid and inexpensive sequencing of complete bacteriophage genomes, using small quantities of nucleic acid as starting material. Feb 18, 2021 · This tool infers the expected genome length of a viral prediction based on the average amino acid identity to a database of complete viral genomes from NCBI and environmental samples. Abstract Bacteriophages are viruses that infect bacteria or archaea Nov 16, 2021 · The annotated genome sequences of all 68 newly isolated phages are available at the NCBI GenBank database under accession numbers listed in S5 Table. However, the ability t … Sep 15, 2022 · Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. About. Nov 11, 2015 · Genome project history. plantarum phages can fill this gap. As of early July 2008, the phage database at NCBI contains 500 genomes ranging from 2. dnam5 archive file. In addition, there is a desire to use phages and their unique proteins for specific biocontrol applications and diagnostics. We use this collection to (i) identify 298 ancient phage Nov 14, 2017 · The primary file DNA Master generates and interacts with is a *. PhagesDB has individual phage pages for each of the more than 8000 phages that have been entered into the database. The extensive repertoire of phages, coupled with the comprehensive genome annotations and sequence comparison results from systematic analyses assisted with fifteen state-of-the-art tools, provide details Jan 19, 2023 · All bacteriophage genomes with the descriptions “complete genomes” or “genomic sequences” were downloaded from the NCBI Genome database (last accessed on May 1, 2022). Built on the Bac Dive model, it gathers and links all the experimental data and metadata (e. 5 If it is important to know the exact termini of the genome, then the choice of sequencing is a critical factor and deciding this Feb 3, 2020 · Phage genomes are composed of either DNA or RNA, which may be double-stranded or single-stranded. It is a distant relative of the well-studied phage P1, but it is sufficiently different that it typifies a previously undescribed tailed phage type or cluster. ebi. PhageScope is an online bacteriophage database that offers comprehensive annotations, including completeness assessment, phenotype annotation, taxonomic annotation, structural annotation, functional annotation, and genome comparison. The method is demonstrated to out-perform both BLAST methods based on single hits and methods based on k-mer comparisons. In viruses as diverse as bacteriophage λ, and the herpesviruses, DNA replication proceeds through a rolling circle mechanism where the circular genome serves as a template for the synthesis of linear concatemers multiple genomes in length. org is a website that collects and shares data, pictures, protocols, and analysis tools associated with the discovery, sequencing, and characterization of mycobacteriophages—viruses that infect the Mycobacteria and also other bacterial hosts in the phylum Actinobacteria. 4%) of the viral genomes were classified as complete, 27,999 (19. ΦFunu1 branches off earlier in the phylogenetic tree and is most closely related to P1, a bacteriophage for Lactobacillus plantarum and the bacteriophage ΦEf11 for Enterococcus Among sequenced viruses in the database, only Pseudomonas phage φKZ , the African swine fever virus, herpesviruses, chlorella virus, and vaccinia virus have larger genomes. gz Place in prokka-1. The T4 genome is a rich arena for evaluating complete genomes in the context of a well-characterized biological system. This article defines 14 questions for those new to phage genomics that should be addressed before submitting a genome sequence to the International Nucleotide Sequence Database Collaboration or writing a publication. g. A reference phage was then selected for each of the 16 genome organizations each to represent the similar phages within each group. Understanding the diverse and intricate genomic architectures of phages is essential to study microbial ecosystems and develop phage therapy strategies. dnam5 files are database files comprised of a genome sequence and multiple tables that contain data about that sequence, including gene start and stop coordinates, functional assignments, BLAST data, etc. Jan 1, 2023 · Summary: In recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences becoming available. jdwjf esr itntiu mcs nnl mkwq dtakwe pfmrd zqhrhvn emss