The UCSC Archaeal Genome Browser: 2012 update

Abstract

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.

Figure 1.

Genome description page layout and feature browsing. (A) An example of a genome information/gateway page that includes genome size, the number of predicted genes, taxonomy, links to publications detailing the species’ isolation and genome sequencing, and links to feature sets available for indexed browsing. (B) The Pfam (6) domains within the genome are displayed in the left frame after clicking on the ‘Pfam protein domains’ link described in Figure 1A. The right frame displays the genomic region of the feature selected from the left frame; in this example, the selected 1-cysPrx_C Pfam domain is displayed within the genome browser.

Figure 2.

Browser tracks available for a sample genome, P. furiosus. (A) GC Percent graph showing the G+C content percentage within a 20-nt sliding window. (B) CRISPR predictions (18,19). (C) NCBI RefSeq (4) protein-coding gene annotations with track elements color-coded to indicate COG functional category (38). (D) Comprehensive Microbial Resource gene annotations (5). (E) Integrated Microbial Genomes gene annotations (23). (F) Protein-coding gene predictions using GeneMark (26), Glimmer (25) and Prodigal (27). (G) Operon predictions from MicrobesOnline (39) and OperonDB (40). (H) Independent gene entries at GenBank. (I) Genomic mappings of Pfam database (6) entries. (J) NCBI conserved domain database (28) search results using RPS-BLAST (29). (K) Non-coding RNA gene annotations from Rfam (17). (L) tRNA gene predictions by tRNAscan-SE (16). (M) NCBI RefSeq (4) non-coding RNA gene annotations. (N) Insertion sequence elements annotated by ISfinder (41). (O) Palindromic transcription factor binding site predictions. (P) Promoter predictions on + strand using 1-nt sliding window of 16-nt BRE/TATA promoter motif scan. (Q) Poly-T motifs as possible transcription termination signals. (R) Ribosomal binding site predictions on + strand using 1-nt sliding window of 10-nt Shine–Dalgarno motif scan. (S) Small RNA sequencing data coverage by Michael Terns and colleagues (42). (T) Microarray expression data showing metabolism of elemental sulfur by Michael Adams and colleagues (43). (U) High similarity nucleotide alignments with other loci in the genome. (V) Paralogs within genome identified by BLASTP search (29). (W) Multiple sequence alignment similarity plot of closely related species using PhyloHMM (12,15). (X) Orthologous gene annotations in closely related genomes based on genome sequence alignments. (Y) Phylogenetic breakdown of BLASTP (29) protein similarities across all proteins within supported archaeal genomes.

Figure 3.

Using the Archaeal COG Browser. The left panel displays the main search interface with search results shown in the table below. Upon clicking on an arCOG link in the results table (in this example, the second entry arCOG00078), a new page displayed in the right panel gives the phylogenetic distribution of proteins within the arCOG (13).