Figure 1.
Definition of the X_HYBRID specificity score. Typical picture of a probe specificity analysis, as available from the MEDIANTE interface (http://www.microarray.fr). Each column represents the number of BLAST hits in the MEDIANTE database (blue), Ensembl database (green), RefSeq database (red) for the BLAST expect-value indicated at bottom. The X_HYBRID score for a probe was calculated as the maximal x_hybrid scores among the three databases. Based on expect-values equal to 10, 1, 10−1, 10−2, 10−3, 10−4, 10−15, 10−20, a ‘rank’ was defined, ranging from 0 for an expect-value equal to 10 to 6 for an expect-value equal to 10−15. For instance, the oligonucleotide depicted in Figure 1 has an extra hit in RefSeq for an expect-value of 10−1, thus defining a rank equal to 2. The number of extra hits between the rank and the lowest expect-value is called delta (Δ). In the example shown in Figure 1, Δ is equal to 1. Δ is always kept in the interval from 1 to 9, meaning that when there are more than 9 extra hits, Δ is kept to 9. A x_hybrid score is defined for each BLAST database (i.e. MEDIANTE, RefSeq, Ensembl) as a decimal number, where the integer part corresponds to the rank, and the leftovers to Δ. The final X_HYBRID score for a probe is defined as the maximal x_hybrid score obtained against the 3 BLAST databases.