domains.INERTIA detects exons with non-neutral evolutionary rates. Transcripts are aligned against related species using three different alignment methods, Kalign (Lassmann and Sonnhammer 2005), multiz (Blanchette et al. 2004), and PRANK (Loytynoja and Goldman 2005), and evolutionary rates of exons for each of the three alignments are contrasted using SLR (Massingham and Goldman 2005).CRASH makes conservative predictions of signal peptides and mitochondrial signal sequences by using locally installed versions of the SignalP and TargetP programs (Emanuelsson et al. 2007) .THUMP makes conservative predictions of trans-membrane helices by analyzing the output of three locally installed trans-membrane prediction methods, MemSat (Jones 2007), PRODIV (Viklund and Elofsson 2004), and PHOBIUS (Kall et al. 2004).CExonic is a locally developed method that uses exonerate (Slater and Birney 2005) to align mouse and human transcripts and then looks for patterns of conservation in exonic structure.CORSAIR is a locally installed method that checks for orthologs for each variant in a locally installed vertebrate protein sequence database.
