![]() For a detailed stepwise command-line approach, est genome assembly, and annotation, we refer the reader to the complementary article “Phage Genome Annotation: where to begin and end” by Shen and Millard in this issue.įIG. We describe some of the available tools and appropriate approaches, based on both web graphical user interfaces and the command-line. High-quality, well-annotated genomes are an essential tool for both basic and applied research and they provide the basis for the identification and annotation of related genomes. We cover guidelines for assembly, structural and functional annotation. Herein, we describe a set of questions to help phage neophytes ensure that their genome assemblies and annotations are of sufficient quality to be sustainable in the long term. These include genomes described as circular, chimeric, and incomplete genomes, genomes in which terminal repeats are found in the middle of the sequence, frame shift assembly errors, as well as poorly or incorrectly described gene products. Lamentably, as more people become involved in bacteriophage research, and phage sequencing becomes more high-throughput and automated, we are observing a significant increase in problems. 6 As such, they are committed to assuring that the sequences of phages submitted to the primary International Nucleotide Sequence Database Collaboration (INSDC) databases (GenBank/EMBL/DDBJ) 7 are of high quality, and that the publications that derive from these submissions are complete and accurate in their annotation and taxonomy. Three of the authors of this article are members of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV). A small error in a sequence database, whether it concerns the length of a protein, an incomplete genome, or an incorrect functional gene annotation can lead to inaccurate interpretations of rapidly increasing sets of metagenomic data. Metagenomics and viromics methods and analyses rely heavily on high-quality genomic databases and annotations to situate metagenome-derived genomes in sequence space. Annotation is not simply about the identification of open reading frames (ORFs) and the putative function of protein-coding genes but should include, in scope, the identification of other functional elements including transfer RNAs (tRNAs), noncoding RNAs, promoters, and terminators.Ībove all, the phage biologist should be aware that errors in assembly can lead to mistakes in annotation that can cause the propagation of inaccuracies in the extant sequence databases. CLC SEQUENCE VIEWER ADD ANNOTATION MANUALHowever, for any such assessment to be accurate it needs to rely on the diligent annotation of the genome using both automated methods and manual curation. The sequencing of phage genomes allows for the delineation of both close and distant relationships within the wider population of phages. 3 Similarly, our understanding that prophages can influence the fitness, phenotype, and global metabolism of the host lysogen necessitates careful identification and annotation of proviral regions within bacterial genomes. The increasing levels of antibiotic resistance in many bacterial nosocomial pathogens have renewed interest in the exploitation of bacterial viruses as therapeutic 1 and biocontrol agents 2 and in the study of the molecular mechanisms underpinning productive infection. For bacteriophages, the accuracy of annotation has never been more important. Comprehensive and accurate genome annotations and critical assessment of genome completeness are crucial facets for the genome sequencing of all organisms. ![]()
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