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