Help
GenomesClick Genomes to see a list of genomes. Results may be sorted by Genome, Taxonomy, Samples, Spectra, and Contig Count by clicking on the column header (alternate between ascending/descending by clicking again).
Individuals may also search for a particular genome by string using the search box near the top (partial matches allowed).
The Taxonomy column shows the species identification for the genome. Click on the species to see the full taxonomic information. In some cases, the species was not identified and will be listed as "unknown species". One can click on "unknown species" to retrieve what taxonomic information is known about that genome.
The Samples column indicates in how many samples the genome was identified. Click on the sample count to see the samples containing this genome and associated study for that sample along with the normalized spectra count for that genome in that sample. Clicking on a specific sample on the 'Samples' page will bring up a list of proteins found within that sample for that genome along with the spectra count for that protein.
The Contig count column indicates how many contigs are contained in the genome. Clicking on a count will bring up a list of contigs for that genome and links to the plots for that contig.
Click Link in the Plots column to see the list of pre-generated plots for that genome. For more information about plots, see the Plots section below in the help.
Click Link in the Files column to see the list of files available to download associated with that genome. Results may be sorted by Genome ID, Download Link, and Type by clicking on the column header (alternate between ascending/descending by clicking again). Click the Download Link link to download the file.
File Types:
- gff: gff data for the genome
- fna: fna data for the genome
- ffn: ffn data for the genome
- missed: missed proteins for prokka or fgs for the genome
- operon: predicted operons for the genome
- spectra: spectra information for samples and proteins for the genome
Click Download to access download files containing various data used for the study analysis. A description for the contents of the file is contained in the Description column.
Plots
The plots shown pregenerated plots for each contig for both FGS and Prokka data. The image should resize to the size of the browser window, but if it does not, open the image in a new tab.
The plots show predicted proteins (PPs) colored in bright purple if they had spectral support in at least two samples or dark purple otherwise.
The plots show open reading frames (ORFs) missed by FGS or Prokka colored in light green.
The plots show validated predicted operons (VPOs) colored in bright blue and non-validated operons (POs) in light blue. See the paper for the methodology on validating operons but these are the operons with spectral support.
ContactContact information for both the paper and issues with the website is available in the footer for each page.
Contact: yye@indiana.edu for questions about the paper or jcandera@indiana.edu for website issues