|Binary Files (*.class) of PSbR||Source Code (*.java) of PSbR||Documentation (*.txt)|
java PSbR [-OPTION] [FILE]The $CLASSPATH environment variable must contain '.' if running it from the actual directory containing the file 'PSbR.class'.
java PSbR -help
java PSbR filename.txtIf the specified file exists and corresponds to the format of the sample-data it is parsed and the permutation is extracted. The resulting permutation is always saved as 'permutation.txt' in the current directory.
java PSbR -random
java PSbR -arbitraryThese options provide the possibility to test the algorithm on randomly shuffled permutations, or on permutations created by a specified number of arbitrary reversals applied on the identity.
We performed experiments on mammalian gene order data extracted from GEM with the RBH (reciprocal best hit) method. Here we provide the SQL request we used, the obtained data, and the permutations that are obtained this way.
The RBH method is well adapted to our model, because it provides a one to one correspondance between genes,
and then data that are immediately transcribed into permutations. However, it often provides false positives
because of duplication events, and there are genes whose position is very unlikely to be the result of a
We then applied a pre-processing to smooth the permutations by deleting putative false orthologs or genes which position reflects other rearrangement events. The pre-processing consists in the following: if a single gene is found between two blocks of contiguous genes in one permutation while these blocks are direct neighbors in the other permutation, the "intruder" gene is deleted in both permutations.
This preprocessing has been joined to the program, and is done before PSbR if the "-p" option is added to the command.