PMC:1852316 / 14814-15748 JSONTXT

{"project":"2_test","denotations":[{"id":"17397539-11160901-1689498","span":{"begin":417,"end":419},"obj":"11160901"}],"text":"We first construct a vector for each gene in E. coli, the dimension of the vector being the number of genomes used in the analysis (in this study 229). We applied BLASTP to identify probable orthologous genes of a target genome in 229 reference genomes. The most significant BLASTP hit from each reference species was considered the true ortholog of the target species if the expectation value was less than 1.0e-10 [25]. If there is an orthologous gene in the ith genome, then the ith entry in this vector is assigned the order of the orthologous gene in the ith genome. If an orthologous gene does not exist in the ith genome, then this entry is taken to be 0. Once such a vector for each E. coli gene is constructed, we compute a phylogenic similarity measure for each gene pair. Given two vectors Xi = [xi1, xi2,...,xi229] for gene i and similarly Xj for gene j, we use the following phylogenic similarity measure for a gene pair:"}