The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical 
web-based resource for exploration and discovery within archaeal and other 
selected microbial genomes. By bringing together existing gene annotations, gene 
expression data, multiple-genome alignments, pre-computed sequence comparisons 
and other specialized analysis tracks, the genome browser is a powerful 
aggregator of varied genomic information. The genome browser environment 
maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but 
also integrates archaeal and bacterial-specific tracks with a few graphic 
display enhancements. The browser currently contains 115 archaeal genomes, plus 
31 genomes of viruses known to infect archaea. Some of the recently developed or 
enhanced tracks visualize data from published high-throughput RNA-sequencing 
studies, the NCBI Conserved Domain Database, sequences from pre-genome 
sequencing studies, predicted gene boundaries from three different protein gene 
prediction algorithms, tRNAscan-SE gene predictions with RNA secondary 
structures and CRISPR locus predictions. We have also developed a companion 
resource, the Archaeal COG Browser, to provide better search and display of 
arCOG gene function classifications, including their phylogenetic distribution 
among available archaeal genomes.