Supplemental Files
Halobacterium salinarum and Haloferax volcanii comparative transcriptomics reveals conserved transcriptional processing sites
Supplemental File S0 (.hbgb files viewer)
Updated version of published by Bare et. al., 2010.
Supplemental File S1
Gaggle Genome Browser file with dRNAseq data and TPS positions in H. salinarum NRC-. Bookmark file for easy navigation is here.
Supplemental File S2
Gaggle Genome Browser file with dRNAseq data, rancRNA and TPS positions in H. volcanii DS2. Bookmark file for easy navigation is here.
Supplemental File S3
GGB file with TEX data at exponential and stationary phases in H. salinarum.
Supplemental File S4
GGB file with Riboseq data and conserved TPS in H. salinarum
Download an updated Gaggle Genome Browser (GGB) software version here (if you still don't have it)
Loading a GGB dataset is as easy as: File > Open dataset
Choose the .hbgb file you want to load.
Now you have it. The GGB rendered all available datasets into an easy to use genome browser.
A Bookmark is an available GGB's feature to annotate a region of the genome with a name, a short description and genomic coordinates to allow quick navigation. Bookmarks are included to features discussed in the paper.
Loading a bookmark flat file into GGB is as easy as: Bookmarks > Load Bookmarks then select the bookmark file you wish to open. You can download our bookmark example file here.
To navigate through all bookmarks, please open the bookmark panel : Bookmarks > Show Bookmarks .
As you can see, navigating through available bookmark elements (right panel) allows you to select a bookmark. A selection will center the GGB main window into the bookmark's genomic positions. (e.g., asTSS-stat-186).
On GGB, all available datasets are rendered as genomic tracks.
Each available track can be shown/hidden. Showing/Hiding a track is as
easy as: Tracks > Visibility and then selecting/deselection the Visible check box field.
As we can see, there are two deselected tracks (Hsalinarum-R1-listofallgenes-OE-halolex-*). Both tracks (rev/fwd) represent Halobacterium salinarum R1 genes that are homologous to Halobacterium salinarum NRC-1 ones.
Selecting this two tracks will render Halobacterium salinarum R1 genes on GGB main window, as displayed below:
Querying features on GGB is straighforward.
Find > find or the shortcut Ctrl+F will open a Search Dialog, which allows you to search terms using wildcard "*".
Search term: *OE3105F (This term is a gene in H. salinarum R1 strain that was not annotated in NRC-1 strain).
Search term: *bacteriorh*
