Download genbank file from patric

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Biochem Biophys Res Commun ; : — Nomenclature for macrolide and macrolide-lincosamide-streptogramin B resistance determinants. Antimicrob Agents Chemother ; 43 : — Missing in action: enzyme functional annotations in biological databases.

Nat Chem Biol ; 5 : — 5. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol ; 5 : e Aminoglycoside modifying enzymes. Drug Resist Updat ; 13 : — Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes. Microbiol Rev ; 57 : — Acquired antibiotic resistance genes: an overview. Front Microbiol ; 2 : Roberts MC. Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes.

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JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol ; 17 : Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account.

Sign In. Advanced Search. Search Menu. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents Abstract. AMR strategy. AMR—integrating data at the genome level. AMR—integrating data at the gene level. Future improvements. Oxford Academic. Rida Assaf. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide.

Sign In or Create an Account. Sign In. Advanced Search. Search Menu. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents Abstract. Gene Graphics: a genomic neighborhood data visualization web application. To whom correspondence should be addressed. Email: katherinejh ufl. Oxford Academic.

Revision received:. Select Format Select format. Permissions Icon Permissions. Abstract Summary. Open in new tab Download slide. Google Scholar Crossref. Search ADS. A family of metal-dependent phosphatases implicated in metabolite damage-control. IMG: The integrated microbial genomes database and comparative analysis system. The subsystems approach to genome annotation and its use in the project to annotate genomes.

Google Scholar PubMed. GenomeDiagram: a python package for the visualization of large-scale genomic data. Experimental and metabolic modeling evidence for a folate-cleaving side-activity of ketopantoate hydroxymethyltransferase PanB.

MicroScope: a platform for microbial genome annotation and comparative genomics. Identification of a novel epoxyqueuosine reductase family by comparative genomics.

Published by Oxford University Press. All rights reserved. A message will appear below the box to indicate that the job is now in the queue.

The results page will consist of a header describing the job and a list of output files, as shown below. These include. After selecting one of the output files by clicking it, a set of options becomes available in the vertical green Action Bar on the right side of the table. View Displays the content of the file, typically as plain text or rendered html, depending on filetype. Allowable types include unspecified, contigs, nwk, reads, differential expression input data, and differential expression input metadata.

More details are available in the Action Buttons user guide. Unlike the Haemophilus influenzae sequence, which is a single finished sequence, the Propionibacterium acnes sequence is a high-quality draft that comprises 17 separate scaffolds.

Each of the 17 scaffold sequences is a separate GenBank entry, and we could download them as separate files, but the simplest approach is to download a single GenBank flat file that contains all 17 sequences and their associated annotation. Recall that this 3-line configuration file displays the coordinate system labels and the gene features, and nothing else.

Note that in this figure we have several gene-free regions, which did not appear in example 1. The reason for this is that we have 17 scaffolds and, by default, Circleator places a 20 kb gap between each pair of adjacent scaffolds or contigs. Circleator has a couple of command-line options that affect the handling of multi-sequence input data. Sequences that are shorter than this will be excluded from the display.

This is why both tracks are visible even though the opacity option was not used. This forces the two to overlap:. The rectangle glyph is a curved rectangle with both a border whose thickness is controlled by the stroke-width and also a filled interior. The two color options color1 and color2 determine what color to draw the border lines and fill the interior:. The next track overlays the accession number of each scaffold on the blue rectangle of the scaffold itself.