Figure 1

Flow chart of the construction of orthologous groups. The diagram represents an overview of our annotation process. We applied four methods of orthologous predictions (BRH, Inparanoid, OrthoMCL and Phylogeny) to 20 fungal genomes. We compared the different groups (represented in the diagram by the sequences S1, S2, S3, S4 and S5) and we constructed their intersections (represented in the diagram by S1, S2 and S3). For each intersection, we aligned the sequences using Muscle [27] and built a HMM profile using HMMER [30]. All these HMM profiles were merged in one file to create a HMM database. Thus, we searched all sequences without a group (S4 and S5 for instance) for shared similarity with one HMM profile (HMMER hmmpfam program) [30]. According to the E-value, we attributed the sequence (E-value ≤ 10^-10) to the corresponding group or excluded it from that group (E-value > 10^-10).