Comparison between predicted and obtained mutations. (a) Output of the CODDLE program using as an example the PsMetI genomic sequence. Exons are represented by white boxes and introns by red lines. The CODDLE program was used to identify those regions of the gene in which G:C to A:T transitions are most likely to result in deleterious effects on the encoded protein (represented by the probability curve traced in tourquoise). The CODDLE algorithm is based on an evaluation of protein sequence conservation from comparison of database accessions of homologous proteins. For PsMetI, three fragments were chosen based on these CODDLE results (blue lines). External and internal primers were designed to amplify each region by nested PCR. (b) Graphic representation of mutations identified in the three regions of the gene PsMetI. This drawing was made using the PARSESNP program , which maps the mutation on a gene model to illustrate the distribution of mutations. Purple triangles represent silent mutations and black and red triangles represent missense and truncation mutations, respectively.
Dalmais et al. Genome Biology 2008 9:R43 doi:10.1186/gb-2008-9-2-r43