BLAST Ring Image Generator (BRIG)

BRIG in action!

Figures generated by BRIG appear in a number of publications. These are a few of our favourites.

From NL Ben Zakour et al. (2012) Analysis of a Streptococcus pyogenes Puerperal Sepsis Cluster by Use of Whole-Genome Sequencing. Journal of Clinical Microbiology. doi: 10.1128/JCM.00675-12

Visualization of the reads selected for each strain mapped onto the S. pyogenes MGAS6180 reference genome. The innermost circles represent the GC content (black), GC skew (purple/green), and rRNA operons of MGAS6180 (pink boxes). BRIG (1) shows the distribution of the number of reads for each individual strain mapped onto the central reference using a window size of 500, arranged from inner to outer colored circles as follows: resequenced reference MGAS6180 (pink), PS001 (yellow), PS006 (orange), PS005 (red), PS007 (maroon), and PS008 (purple). Additional strain-specific regions of difference (RODs) (ϕPS008 and ICESpPS008) are represented as insertions. The outermost circle represents previously reported regions of difference in MGAS6180, namely, prophage elements 6180.1 and 6180.2, prophage remnants 6180.3 and 6180.4, and regions of difference 6180.RD1 and 6180.RD2 (15) (black).

From Q Huang et al. (2012) High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria. PLoS ONE 7(3): e33759. doi:10.1371/journal.pone.0033759

BRIG diagram showing results of GIST and Islandviewer on Salmonella enterica 62:z4,z23:– RSK2980 (NC_010067).
GIs predicted with Islandviewer are marked as Island1, Island2, etc.; and those predicted by GIST are denoted with Gist1, Gist2, etc. The three main divergent regions detected by GIST but missed by Islandviewer are labeled with green triangles.

 

From KYL Chua et al (2011) The Dominant Australian Community-Acquired Methicillin-Resistant Staphylococcus aureus Clone ST93-IV [2B] Is Highly Virulent and Genetically Distinct. PLoS ONE 6(10): e25887. doi:10.1371/journal.pone.0025887
N.B ONLY FIGURE B was generated with BRIG.

Whole genome sequence analysis and comparison of JKD6159 with other S. aureus strains.
(A) Artemis linear view of JKD6159 chromosome, with vertical red bars identifying the position of accessory genome elements as determined by read mapping against 19 publicly available completed genomes and 62 unpublished, partially assembled genome sequences. Increasing height of vertical red lines indicates increasing specificity for JKD6159. Shown above the accessory genome analysis are the mapped positions of the short-reads obtained from Illumina sequencing CA-MRSA strains JKD6177, JKD6272 and JKD6260. Depicted also is an example of the synthetic reads obtained from completed whole genome sequences (USA300 shown here) to facilitate the comprehensive read mapping approach described in the methods. (B) Circular diagram of the JKD6159 chromosome showing (from inner to outer), % G+C, GC skew and the homology based on BLASTn+ analysis of JKD6159 to 19 completed S. aureus genomes (refer color-coded legend). Outer circle shows the location of accessory elements (grey) and the 12 regions of difference (blue) not present in the other S. aureus genomes examined.
doi:10.1371/journal.pone.0025887.g003

From M Totsika et al (2011) Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms. PLoS ONE 6(10): e26578. doi:10.1371/journal.pone.0026578

Genomic map of ST131 E. coli EC958.
The inner circle represents the reference sequence, E. coli EC958, with scaffolds of the draft assembly displayed as alternating blue or red color in the inner-most ring. Outer rings show shared identity (according to BLASTn) with individual UPEC genomes and various other E. coli genomes. BLASTn matches between 80% and 100% nucleotide identity are colored from lightest to darkest shade, respectively, according to the graduated scale on the right of the circular BLAST image. Matches with less than 80% identity, or E. coli EC958 regions with no BLAST matches, appear as blank spaces in each ring. Rings indicate BLAST identity, from inside to out, between EC958 and: (1–5) individual UPEC genomes CFT073, 536, UTI89, IAI39, UMN026 (light to dark blue); (6) pooled ExPEC genomes: APEC O1, IHE3034, S88 (purple); (7) pooled EHEC/EPEC genomes: EC4115, Sakai, EDL933, E2348 (pink); (8) pooled EAEC/AIEC/ETEC genomes: 55989, O42, LF82, E24377A (yellow); (9) environmental E. coli genome: SMS_3_5 (lime green); (10) pooled commensal E. coli genomes: IAI1, SE11, SE15, HS, 8739, ED1a (teal); pooled E. coli K12 genomes: MG1655, W3110, DH10B (green). Black labels indicate regions that are known to be variable in E. coli genomes. Blue labels and arcs indicate RODs that appear to be prophage regions; red labels and arcs indicate known genomic islands (GI-pheV, GI-selC, GI-thrW, and GI-leuX) or potential new genomic islands (ROD1–3). The image was prepared using Blast Ring Image Generator (http://sourceforge.net/projects/brig).
doi:10.1371/journal.pone.0026578.g001

Written by Nabil-Fareed Alikhan

July 10th, 2012 at 12:59 am

Posted in