Cassis: Detection of genomic rearrangement breakpoints

The package Cassis implements methods for precise detection of genomic rearrangement breakpoints, which were described in Lemaitre et al., 2008 [3].

1 - Requirements

2 - Download

     The package is free and licensed under the GNU General Public License.

     The package can be downloaded here: cassis.zip

3 - Installation instructions

  1. Download the package

  2. Unzip the downloaded file cassis.zip
    > unzip cassis.zip
    This command will create a directory named cassis which contains all package scripts.

  3. Download LASTZ

  4. Compile LASTZ and copy the generated executable file (lastz) to the directory cassis/lastz.

  5. Download and Install R

4 - Software documentation

     The documentation with description of the methods can be downloaded here: cassis_manual.pdf (Last update: 25/02/2013.)

5 - Case study - Running cassis with Homo sapiens and Mus musculus orthologous genes

     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.

6 - Running cassis with orthologous synteny blocks

     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):

7 - Comparing Cassis with other methods for detecting breakpoints

     As far as we know, the current methods for detecting breakpoints (Mauve [1], GRIMM-synteny[5], Magic [6], 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.

References

  1. 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

  2. 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.

  3. 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.

  4. Harris, R. S. (2007). Improved pairwise alignment of genomic DNA. Ph.D thesis. The Pennsylvania State University, 84 pages.

  5. Pevzner P. and Tesler G. (2003). Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Research, 13, 37-45.

  6. 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.



Last update: 25/02/2013.