DRIMM - Duplication and Rearrangement in Multiple Mammals

Computer Science and Engineering Department, UCSD.

DRIMM

DRIMM algorithm extends the GRIMM-Synteny (Genome Rearrangements in Men and Mice) algorithm towards the problem of identifying the synteny blocks in highly duplicated genomes.

Info: A version of DRIMM-Synteny for linux to be released.

The algorithm devises the first A-Bruijn graph approach that does not require a threading step and substituting it with an alternative genome transformation step implemented in the DRIMM-Synteny. Please subscribe to the mailing list to receive latest information as well as supports

Yeast

S. cerevisiae and K. waltii :

The raw data for S. cerevisiae and K. waltii comparison is extracted from Kellis's supplementary files by Max Alekseyev.. The input was further processed to change the gene anotation to numbers, i.e., two homologous gene will have the same geneID. The preprocessed data can is used as the input for the program. The first eight lines are the chromosomes of K. waltii, while the rest are the chromosomes of S. cerevisiae.

Result:

1. Synteny blocks

2. DRIMM paired regions vs. Kellis paired regions.

S. cerevisiae and A. gossypii

The raw data for S. cerevisiae and A. gossypii comparison is provided by Max Alekseyev.. The input was further processed to change the gene anotation to numbers, i.e., two homologous gene will have the same geneID. The preprocessed data can is used as the input for the program. The first eight lines are the chromosomes of A gossypii, while the rest are the chromosomes of S. cerevisiae.

Result:

1. Synteny blocks

 

S. cerevisisae

Result:

1. Synteny blocks

Supplementary information

Program:

The program is written in C# and used Test Driven Development methodology.

The source code of the program can be downloaded here

Contact: Son K. Pham kspham @at@ cs.ucsd.edu

Mamalian genomes

1. Human-Chimpanzee-Macaque:

The raw data for Human, Chimpanzee and Macaque is provided by Tao Jiang. The input was further processed to change the gene anotation to numbers, i.e., two homologous gene will have the same geneID.

Results:

1. Synteny blocks: Human-Chimpanzee-Macaque

2. Synteny blocks: Human-Chimpanzee

3. Synteny blocks: Human-Macaque

 

2. Human-Chimpanzee-Macaque-Rat-Mouse-Opossum-Cow

Result: Synteny blocks

1. Shared by 7 species

H-C-M-R-Mo-O-Co

2. Shared by 6 species:

A. H-C-M-R-Mo-Co

B. H-M-R-Mo-O-Co

C. H-C-M-Mo-O-Co

3. Shared by 5 species

A. H-C-M-R-Mo

B. H-C-M-O-Co

4. Shared by 4 species

A. H-C-M-Co

5. Shared by 3 species

A. H-C-M

 

Genome of Arabidopsis:

We run the DRIMM-Synteny for the Arabidopsis genome.

The synteny blocks have multiplicity of 2, 3 and 4:

A. Multiplicity of 2

B. Multiplicity of 3

C. Multiplicity of 4