Mercator files specify an orthology map between multiple genomes: a symmetric, 1-to-1 mapping between regions in different genomes.
The Mercator program creates this map by extending cliques of orthologous exons into syntenic runs.
Local alignment programs (PECAN, MAVID, FSA) are typically then run on each syntenic region, producing an alignment for each line in the Mercator map file.
Two files are actually needed: map (containing the co-ordinates) and genomes (specifying the order of genomes in map).
- Mercator program by Colin Dewey
- Format of the map and genomes files:
- References for Mercator:
- Dewey &: Aligning multiple whole genomes with Mercator and MAVID. Methods Mol. Biol. 2007;395:221-36.
- Chapter 3 & Appendix A of Whole-Genome Alignments and Polytopes for Comparative Genomics, Colin Dewey, EECS Department, University of California, Berkeley. Technical Report No. UCB/EECS-2006-104