The BOBRO download page can be accessed at Project Homepage.
This software provides a tool capable of accurately extracting cis-regulatory motifs with their correct lengths even in thousands of promoters from a whole prokaryotic genome. For a fasta file containing promoters, the program outputs a number of profiles containing the binding sites of specific motifs.
Certain parts of the code uses open-source data structure library codes, including:
Note
BOBRO currently will only run on linux platform, as it is dependent on GNU function (version 3.3.3).
Simply put “BoBro0.1.tar.gz” in any directory:
$ tar zxvf BoBro0.1.tar.gz
enter the folder BoBro0.1 and type make, the compiled codes are within the same directory (folder 'bin') as the source.
The major program in the provided package is BOBRO, it can parse files of fasta format and an example is provided. See help and look at all available options.
$ ./BOBRO -h
Take a look at example (fasta format) first. And try to run BOBRO:
$ ./BOBRO -i example -l 14
For each input file under a specific length l, our program generates two output files, namely,'.seeds' file and '.closures'file. In '.seeds' file you can see all the motif seeds ranked by their size (number of their binding sites); as to '.closures' file, it provides all the closures generated by the motif seeds in the increasing order of their pvalues.
Then try to run BOBRO recognizing the correct length in the scope [L,U] by our program automatically.
$ ./BOBRO -i example -L 14 -U 16
L and U are the low boundary and up boundary of the scope of length separately. We use this pair of parameters when we do not know the accurate length in advance. Here we also generate the '.seeds' file and '.closures' file mentioned above, storing the corresponding information under all possible length. In addtional, we generate one output file, namely, '.auto' file which containing the closures, with the smallest pvalue under each specific length, in the increasing order of their pvalues. Especially, when the input value of L equals to U, it is equivalent to finding motifs in a specific length. '$ ./BOBRO -i example -L 14 -U 14' is equivalent to '$ ./BOBRO -i example -l 14'.
Any questions, problems, bugs are welcome and should be dumped to