text: user3061: I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence file to an object that can be used in Gviz? I searched the user guide and the reference manual. It is stated that it is possible to use fasta file, but not how to use them.
  We will generate lots of genomes that we will have to annotate and compare. S aureus is not S aureus. There is a spectrum of phenotypes, they all have a different genomes. And we will also not be limited to SA. The question here is not how to annotate the genome, but rather the steps necessary to visualize something and get going. It is my first steps with genomic data, I don't even know what makes sense.
  Here is the head of the file:
  >NC_007795.1 Staphylococcus aureus subsp. aureus NCTC 8325 chromosome, complete genome
  CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGGTCCGAAGCATGAGTGTTT
  ACAATGTTCGAACACCTTATACAGTTCTTATACATACTTTATAAATTATTTCCCAAACTGTTTTGATACACTCACTAACA
  GATACTCTATAGAAGGAAAAGTTATCCACTTATGCACATTTATAGTTTTCAGAATTGTGGATAATTAGAAATTACACACA
  AAGTTATACTATTTTTAGCAACATATTCACAGGTATTTGACATATAGAGAACTGAAAAAGTATAATTGTGTGGATAAGTC
  GTCCAACTCATGATTTTATAAGGATTTATTTATTGATTTTTACATAAAAATACTGTGCATAACTAATAAGCAAGATAAAG
  TTATCCACCGATTGTTATTAACTTGTGGATAATTATTAACATGGTGTGTTTAGAAGTTATCCACGGCTGTTATTTTTGTG
  TATAACTTAAAAATTTAAGAAAGATGGAGTAAATTTATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCA
  AGAAAAATTATCAGCTGTAAGTTACTCAACTTTCCTAAAAGATACTGAGCTTTACACGATTAAAGATGGTGAAGCTATCG
  TATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATTATCCAAGCAATCTTATTTGATGTT
  
  
  user96: I am not familiar with Gviz, but I am familiar with a variety of tools for visualizing genome features. At the scale of entire microbial genomes, the primary sequence itself is an overwhelming amount of information and can't really be visualized in a meaningful way by itself. I mean, you could color the nucleotides, but few patterns in DNA can be discerned by an unassisted human eye.
  What we're typically interested in are features encoded in the genome sequence: protein-coding genes, non-coding RNAs, transposable elements, regulatory elements, binding sites, epigenetic modifications, and so on. A particular scientist is usually only interested in a subset of these features, based on what particular questions they are investigating. In your comment you say you "would like to annotate protein coding regions and compare them to other genomes", so it seems like we're on the same page here.
  Visualization tools often display the genome linearly (even, for example, if it's a circular bacterial chromosome), zoomed out so that the nucleotide sequence isn't visible, and overlayed with boxes, arrows, or other glyphs representing the genes or other features of interest. Here are some examples:
  
  This question thread contains images generated with the GenomeTools AnnotationSketch program (gt sketch command).
  The UCSC genome browser which provides web-based access to dynamic displays of the human genome and many other mammalian genomes.
  The IGV browser can be downloaded and easily run on your personal laptop or desktop computer.
  I'm not familiar with Gviz, but it definitely looks like it belongs in this class of tools.
  
  In each of these cases, the visualization software is not doing the work to determine the positions of the genes and other genome features. This was done independently using tools designed for this task, storing the information in an annotation file in GFF3, GTF, or BED format. The visualization tools need both the genome sequence (in Fasta format) and one or more annotation files (in GFF3, GTF, or BED format) to make meaningful visualizations.
  
original_text: 3061: <p>I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence file to an object that can be used in Gviz? I searched the user guide and the reference manual. It is stated that it is possible to use fasta file, but not how to use them.</p>
  
  <p>We will generate lots of genomes that we will have to annotate and compare. S aureus is not S aureus. There is a spectrum of phenotypes, they all have a different genomes. And we will also not be limited to SA. The question here is not how to annotate the genome, but rather the steps necessary to visualize something and get going. It is my first steps with genomic data, I don't even know what makes sense.</p>
  
  <p>Here is the head of the file:</p>
  
  <pre><code>&gt;NC_007795.1 Staphylococcus aureus subsp. aureus NCTC 8325 chromosome, complete genome
  CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGGTCCGAAGCATGAGTGTTT
  ACAATGTTCGAACACCTTATACAGTTCTTATACATACTTTATAAATTATTTCCCAAACTGTTTTGATACACTCACTAACA
  GATACTCTATAGAAGGAAAAGTTATCCACTTATGCACATTTATAGTTTTCAGAATTGTGGATAATTAGAAATTACACACA
  AAGTTATACTATTTTTAGCAACATATTCACAGGTATTTGACATATAGAGAACTGAAAAAGTATAATTGTGTGGATAAGTC
  GTCCAACTCATGATTTTATAAGGATTTATTTATTGATTTTTACATAAAAATACTGTGCATAACTAATAAGCAAGATAAAG
  TTATCCACCGATTGTTATTAACTTGTGGATAATTATTAACATGGTGTGTTTAGAAGTTATCCACGGCTGTTATTTTTGTG
  TATAACTTAAAAATTTAAGAAAGATGGAGTAAATTTATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCA
  AGAAAAATTATCAGCTGTAAGTTACTCAACTTTCCTAAAAGATACTGAGCTTTACACGATTAAAGATGGTGAAGCTATCG
  TATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATTATCCAAGCAATCTTATTTGATGTT
  </code></pre>
   96: <p>I am not familiar with Gviz, but I am familiar with a variety of tools for visualizing genome features. At the scale of entire microbial genomes, the primary sequence itself is an overwhelming amount of information and can't really be visualized in a meaningful way by itself. I mean, you could color the nucleotides, but few patterns in DNA can be discerned by an unassisted human eye.</p>
  
  <p>What we're typically interested in are features encoded in the genome sequence: protein-coding genes, non-coding RNAs, transposable elements, regulatory elements, binding sites, epigenetic modifications, and so on. A particular scientist is usually only interested in a subset of these features, based on what particular questions they are investigating. In your comment you say you "<em>would like to annotate protein coding regions and compare them to other genomes</em>", so it seems like we're on the same page here.</p>
  
  <p>Visualization tools often display the genome linearly (even, for example, if it's a circular bacterial chromosome), zoomed out so that the nucleotide sequence isn't visible, and overlayed with boxes, arrows, or other glyphs representing the genes or other features of interest. Here are some examples:</p>
  
  <ul>
  <li><a href="https://bioinformatics.stackexchange.com/q/5171/96">This question thread</a> contains images generated with the <a href="http://genometools.org/annotationsketch.html" rel="nofollow noreferrer">GenomeTools AnnotationSketch program</a> (<code>gt sketch</code> command).</li>
  <li>The UCSC genome browser which provides web-based access to <a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&amp;lastVirtModeType=default&amp;lastVirtModeExtraState=&amp;virtModeType=default&amp;virtMode=0&amp;nonVirtPosition=&amp;position=chr1%3A11102837%2D11267747&amp;hgsid=706397415_aaU7aADCAPm3vbNa7iTImwAxTqcu" rel="nofollow noreferrer">dynamic displays of the human genome</a> and many other mammalian genomes.</li>
  <li>The <a href="http://software.broadinstitute.org/software/igv/" rel="nofollow noreferrer">IGV browser</a> can be downloaded and easily run on your personal laptop or desktop computer.</li>
  <li>I'm not familiar with <a href="https://bioconductor.org/packages/release/bioc/html/Gviz.html" rel="nofollow noreferrer">Gviz</a>, but it definitely looks like it belongs in this class of tools.</li>
  </ul>
  
  <p>In each of these cases, the visualization software is not doing the work to determine the positions of the genes and other genome features. This was done independently using tools designed for this task, storing the information in an <strong>annotation</strong> file in <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md" rel="nofollow noreferrer">GFF3</a>, <a href="http://mblab.wustl.edu/GTF22.html" rel="nofollow noreferrer">GTF</a>, or <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1" rel="nofollow noreferrer">BED</a> format. The visualization tools need both the genome sequence (in Fasta format) and one or more annotation files (in GFF3, GTF, or BED format) to make meaningful visualizations.</p>
  