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Figure 1 | BMC Bioinformatics

Figure 1

From: Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis

Figure 1

Description of the methods used in the "Gene Function Predictor". The protein coding genes of our target organism E. coli are compared to the ORFs of 150 genomes. (A) The P score applied to E. coli protein phylogenetic profiles allows to identify protein pairs that evolved in a similar manner. For example, genes A and E are present in genomes 1, 2 and 150 and absent in genome 3. (B) The C score is associated to gene pairs nearby in, at least, one genome. This score is computed from the intergenic distances between E. coli genes and their respective homologs in all other genomes. The genes B and F (respectively red and green) are found only separated by 30 bp in genome 1 and by 5 bp in genome 3, resulting in a C score of 0.8 between those two genes. (C) The F score is computed for each domain fusion detected. In the example, domains of E. coli genes C and D are found fused in a gene of genome 3. (D) Significant P, C and F scores are combined in an integrated score. (E) Functional predictions are made out of the annotations of associated partners.

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