Ultra-Conserved Elements in Vertebrate and Fly Genomes

Our analyses of ultra-conserved elements are based on multiple sequence alignments produced by MAVID [Bray and Pachter, 2004]. Prior to the alignment of multiple genomes, homology mappings (from Mercator [Dewey, 2005]) group into bins genomic regions that are anchored together by neighboring homologous exons. A multiple sequence alignment is then produced for each of these alignment bins. MAVID is a global multiple alignment program, and therefore homologous regions with more than one homologous hit to another genome may not be found aligned together. Table 22.1 shows an example of Mercator’s output for a single region along with the beginning of the resulting MAVID multiple sequence alignment.