Evolutionary Breakpoints Analyser (EBA)
Thanks for your interest in EBA.
The EBA algorithm is for precise detection of chromosomal breakpoint region in assembled to chromosome or genome sequences. These genomic rearrangement breakpoints regions were classified and assigned to phylogenetic nodes, which were described in manuscript and supplementary.
Term definitions:
Homologous Synteny Block (HSB) refer to two or more homologous markers (genes, sequences) that are syntenic in two or more species, have the same order, and are not interrupted by any other HSB.
Evolutionary Breakpoint Region (EBR), a region between two homologous synteny blocks that is demarcated by an evolutionary chromosome breakpoint boundary on each side.
1. Software documentation and manual
The EBA documentation with detail description of each flags to run and EBA can be downloaded here: EBA_manual.pdf (Last update: 23/06/2015.)
2. EBA Case study
In order to check the EBA breakpoint analysis capability, it is being run with 6 Mammalian and 6 Avian genome synteny block sets.
To demonstrate the advantages of EBA, we conducted an experiment with a real cattle HSB data set. We obtained the cattle synteny dataset from the cattle genome sequencing consortium and we used synteny blocks as an input for our EBA analysis.
You can access the results of this real data set study at <>.
2.1 Running EBA with mammalian synteny blocks
The EBA incorporated the flags for processing the phylogenetic classification of all studied species using the NCBI taxonomy database. With this feature, EBA process the list of all studies species and produced the classification file. Later, they used the synteny blocks to detect the EBRs and assign each one of them to phylogenetic node and, consequently, identify and refine GAPs, reuse and other breakpoints.
To illustrate EBA functionality, we processed two different sets of mammalian synteny blocks:
Human data
Chicken data
2.2 Comparing both analysis with other methods
Here we present a comparison between the results of the executions of EBA with mammalian and avian synteny blocks. The result shows that EBA is able to correctly detect EBRs and classify them irrespective of reference and resolutions.
You can find the detail data at <>
3. Download EBA
The EBA tool and supporting scripts are free and licensed under the GNU General Public License.
The EBA tool and related scripts can be downloaded here: EBA.zip
We are working hard to make it available for public usage. Will be available online for academic use soon.
Visit next time.
Cheers
EBA Team
