Whole-Genome Homology Maps (Old methods)

[Introduction] [Terminology] [Methods] [Downloads] [Acknowledgements] [References]


Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms "homologous", "orthologous", and "paralogous" instead. Ideally, given N genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence. Presented here is initial work on creating an orthology map for the human, mouse, and rat genomes.


The length of the smallest rearrangement that is identified by the map.
The maximum length of mapped regions for each map piece. Segmented maps are useful for comparative programs that require smaller input sizes.



Lines in the map files are of the form:
 [Segment Label] [Piece #] [Chrom] [Start] [End] [Strand] ...  
where the last 4 fields are repeated for each genome in the map. The fields are tab-delimited. For coordinates on the reverse strand "-", the start coordinate is greater than the end coordinate. Pieces for which no orthologous region could be identified in one of the genomes have "NA" in the fields for the appropriate genomes. The order of the genomes in each line is given by the order of the genomes in the name of the map file.