The orthology information in YEASTRACT+ was obtained using the Reciprocal Best Score (RBS) BLAST approach. The detailed methodology is presented below.

Methodology

1. The proteome of each species was used as the input for a BLASTp, using a p-value of 1e-5 and performed in a reciprocal way between all the species of the DB.
2. The BLAST hit with the highest score for each protein sequence is considered as the BEST hit. Additionally, a tolerance of 10% is applied, meaning that alignments with a score almost identical to the best-score are not lost.
3. At this stage the homology is obtained.
4. This information is crossed with the synteny by comparing the genes adjacent to each homolog locus. 15 neigbors are considered in each direction.
5. 3 levels of synteny "strength" were created, by requiring a minimum of 1, 2 or 3 neighbor genes in common.