The eight modules are as follows (see Supplementary Data for further details). Matador3D checks for the presence of structural homologs in the PDB (20) and tests the integrity of the 3D structure; firestar (19) makes highly reliable predictions of conserved functionally important amino acid residues; SPADE uses the program Pfamscan (21) to count conserved and compromised Pfam functional domains; INERTIA uses three alignment methods (22–24) to generate cross-species alignments, from which SLR (25) identifies exons with unusual evolutionary rates; CRASH makes conservative predictions of signal peptides using the SignalP and TargetP programs (26); THUMP generates conservative predictions of trans-membrane helices from three separate trans-membrane predictors (27–29); CExonic uses exonerate (30) to align mouse and human transcripts and looks for patterns of conservation in exonic structure and CORSAIR uses BLAST (31) to map vertebrate orthologs to each variant and counts the numbers of orthologs that align correctly and without gaps. All of these methods are available as web services.
