The UCSC Archaeal Genome Browser

Abstract

As more archaeal genomes are sequenced, effective research and analysis tools are needed to integrate the diverse information available for any given locus. The feature-rich UCSC Genome Browser, created originally to annotate the human genome, can be applied to any sequenced organism. We have created a UCSC Archaeal Genome Browser, available at http://archaea.ucsc.edu/, currently with 26 archaeal genomes. It displays G/C content, gene and operon annotation from multiple sources, sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-genome alignments and protein conservation across phylogenetic and habitat categories. We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the archaeal research community.

Figure 1

The intergenic region denoted Pfu.i140, located between P.furious ORFs PF0216 and PF0217, shows high conservation among closely related species (‘Conservation’ track), high ‘G/C Percent’ values (indicative of RNA structure in hyperthermophiles), and a different expression pattern from the neighboring ORFs (green: suppressed relative to baseline, red: induced relative to baseline in a heat shock time course). The ‘Promoter +’ track with green peaks indicates a TATA box that is ∼88 bp upstream of PF0217, not the −38 position that is typical for this species. Together, these pieces of evidence suggest that transcription starts 50 bp upstream of the predicted coding region, which implies one of three possibilities: (i) this is a non-coding RNA gene that is co-transcribed with PF0217 but later processed away from the transcript; (ii) this is a regulatory UTR of PF0217 with secondary structure; or (iii) the start codon is incorrectly annotated forPF0217.