D264 Nucleic Acids Research, 2009, Vol. 37, Database issue Figure 3. The new PeroxiScan interface and result. PeroxiScan tool enables the identiﬁcation of a given peroxidase sequence. PeroxiScan can be performed directly from one entry or independently from the ‘Tools’ section for an unknown sequence. Fine descriptions of the matching scores are available from a direct submission through MyHits web site. the whole conserved region of each subfamily, but to make the proﬁle more speciﬁc, residues that are conserved in the whole family are lightened and residues speciﬁc to each subfamily are emphasized. We started by merging all families that overlap to construct general alignments. In these alignments, we speciﬁcally tag well-conserved resid- ues. The family alignments are then simply split (without modifying the alignment of residues) in several sub-alignments according to our subfamily classiﬁcation. Each subfamily alignment now contains an annotation line where residues conserved in the whole family and residues speciﬁc to the subfamily are tagged. This annotation line is then used by our proﬁle construction program to down weigh family-conserved columns and over weight subfamily-speciﬁc ones (see http://www.expasy.org/tools/ subproﬁler/subproﬁler_help.html for more details).