Using BRIG to compare a multi-sequence reference against complete genomes or unassembled sequence reads. BRIG image showing the presence, absence and variation of individual genes from the E. coli O157:H7 str. Sakai Locus of Enterocyte Effacement (LEE) in related pathogens and E. coli K12, a non-pathogenic strain of E. coli known to lack the LEE region. Images show a multi-sequence reference consisting of the translated nucleotide sequences of the 41 LEE protein-coding genes, in order, retrieved from the E. coli O157:H7 str. Sakai genome [GenBank: BA000007]. Labels around the outside of each circular image correspond to LEE gene names. In both panels the rings display BLAST× comparisons of 10 bacterial genomes with the translated nucleotide sequences of the LEE genes: A. Comparison with complete genome sequences (Table 2). B. Comparison with unassembled, simulated 100 base-pair Illumina reads based on the complete genome sequences used in Figure 3A. The image is scaled to the nucleotide length of the genes. Long tick marks on the outer and inner circumference of the ring indicate increments of 1 kilobase-pairs and short tick marks indicate 200 base-pairs.