Tip of the Week: Chromhome, for karyotype level comparative genomics
Usually when we think about comparative genomics data, we are thinking about genomes that are pretty well sequenced, and we want to look at that data with variety of tools and algorithms. But this past week we saw a question about less-well-sequenced genomes, and we thought it was an interesting inquiry. The question was: is there a web site that displays comparative karyotype data? So we went looking. And we found Chromhome.
Chromhome has a very straightforward interface. You choose a target species. You choose the probe species. You click paint–and you get a look at the chromosome level homology. When the data was performed with actual probes and reported in the literature, that data is provided. At the time the paper was published this consisted of more than 100 data sets.
There is also the opportunity to see inferred painting as well. I’ll let the Chromhome paper authors describe that strategy:
If species A and species B are mapped on species N, then it is possible to deduce some of the chromosomal arrangements of A on B or B on A with respect to the arrangements of N chromosomes. Many of the species in Chromhome have been mapped on human chromosomes using chromosome painting. It is therefore possible to infer homologies between two species each of which have been hybridized with human probes.
So if this type of comparative genomics may be of interest to you, check out Chromhome.
Nagarajan, S., Rens, W., Stalker, J., Cox, T., & Ferguson-Smith, M. (2008). Chromhome: A rich internet application for accessing comparative chromosome homology maps BMC Bioinformatics, 9 (1) DOI: 10.1186/1471-2105-9-168