Searching the GTDB database for a gene/protein of interest
This example shows the results of searching the McrA protein sequence against the archaeal database.
E-value=0.00001, coverage threshold=50%. Final hits were refined by choosing hits in the Methanosarcina genus.
Sequence used for search: P07962 MCRA_METBF.
Search for gene neighborhoods of McrA (Methyl-coenzyme M reductase subunit alpha) homologs in the Methanosarcina genus.
Uploading a custom dataset of gene neighborhoods derived from the NCBI
This example visualizes gene neighborhoods surrounding Slr4 (a type of S-layer protein discovered by Ali et al., 2020) genes in Gammaproteobacteria.
Gene neighborhood information was extracted from the NCBI database as shown in Github.
Visualization of larger sequences (contigs, plasmids, viral genomes, bacterial genomes)
Although we do not currently support visualization of large (e.g., eukaryotic) genomes, AnnoView can be used to visualize smaller genomes or genomic regions. The examples below show the use of AnnoView in exploring an alignment of betacoronavirus genomes, as well as the genome and plasmid of Clostridium tetani.
Visualization of the entire C. tetani genome.