The package Cassis implements methods for precise detection of genomic rearrangement breakpoints, which were described in Lemaitre et al., 2008 .
The package is free and licensed under the GNU General Public License.
The package can be downloaded here: cassis.zip
Download the package
Unzip the downloaded file cassis.zip
> unzip cassis.zip
This command will create a directory named cassis which contains all package scripts.
Compile LASTZ and copy the generated executable file (lastz) to the directory cassis/lastz.
Download and Install R
The documentation with description of the methods can be downloaded here: cassis_manual.pdf (Last update: 25/02/2013.)
To demonstrate the advantages of Cassis, we conducted an experiment with a real data set.
We obtained from Ensembl the list of one-to-one orthologous genes which are found in the genomes of Homo sapiens and Mus musculus and we used it as input for our package.
Here you can access the results of this study.
Cassis incorporated the option of processing lists of orthologous synteny blocks. With this feature, we can process the list of synteny blocks produced by other methods and, consequently, identify and refine the breakpoints.
To illustrate this functionality, we processed two different sets of orthologous synteny blocks (Homo sapiens and Mus musculus):
As far as we know, the current methods for detecting breakpoints (Mauve , GRIMM-synteny, Magic , etc.) are in fact procedures for detecting synteny blocks. The breakpoint regions are provided as a byproduct, simply by identifying intervals which are not covered by the synteny blocks. The method implemented in Cassis aims to go one step further and to extend the synteny blocks by focusing on the breakpoints themselves.
Here we present a comparison between the results of the executions of Cassis with one-to-one orthologous genes and one-to-one orthologous synteny blocks (Compara and Mauve) and we show that Cassis is able to refine substantially the breakpoint locations.
Darling A. C. E., Mau B., Blattner F. R., and Perna N. T. (2004). Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. Genome Research, 14, 1394-1403
Lemaitre, C. (2008), Réarrangements chromosomiques dans les génomes de mammifères: caractérisation des points de cassure. Ph.D thesis, Université Claude Bernard - Lyon 1, 180 pages, In French.
Lemaitre, C., Tannier, E., Gautier, C., and Sagot, M.-F. (2008). Precise detection of rearrangement breakpoints in mammalian chromosomes. BMC Bioinformatics, 9(286), 15 pages.
Harris, R. S. (2007). Improved pairwise alignment of genomic DNA. Ph.D thesis. The Pennsylvania State University, 84 pages.
Pevzner P. and Tesler G. (2003). Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Research, 13, 37-45.
Swidan F., Rocha E. P. C., Shmoish M., and Pinter R. Y. (2006). An Integrative Method for Accurate Comparative Genome Mapping. PLoS Computational Biology, 2(8), 16 pages.