| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| remove_trash.pl | 2018-03-19 | 3.5 kB | |
| tetrad.txt | 2018-03-19 | 152 Bytes | |
| triple.txt | 2018-03-19 | 108 Bytes | |
| two.txt | 2018-03-19 | 53 Bytes | |
| comb4.cc | 2018-03-19 | 17.8 kB | |
| readme.txt | 2018-03-19 | 2.1 kB | |
| comb2.cc | 2018-03-19 | 16.4 kB | |
| comb3.cc | 2018-03-19 | 17.1 kB | |
| Totals: 8 Items | 57.3 kB | 0 |
=========================================== Release notes for PBlock version 1.0 =========================================== This software is free, open source software released under the GNU General Public License. This software consists of three parts. The first part named remove_trash.pl is written in Perl script aiming for remove redundant substrates. The second part named uncooperative.cc is written in C++ script aiming for finding and calculating the weight of the combinations of given two sites in the complete graph. The third part is composed of three sections, named comb2.cc,comb3.cc and comb4.cc, aiming for finding the significant combinations and calculating the proportions of significant combiantions in the corresponding type in two-tuples, triples and tetrads. . This software is free to use, modify, redistribute without any restrictions, except including the license provided with the distribution. =========================================== Instruction =========================================== (1) Download the amino acid residues at site P4-P4' of the substrate dataset of the protease from the MEROPS database. (2) Run remove_trash.pl to remove redundant substrates to make sure that there is no pair of sequences whose similarity is above 0.875(the default value), this step can be skipped by the user if the dataset is preprocessed. (3£© Run comb2.cc,comb3.cc and comb4.cc respectively, output the significant combintions and the proportions in three types. The default random time is 1000. The columns of amino acid residues at site P4-P4' are indexed by number 1-8 from left to right, and the corresponding columns of three types are listed in two.txt, ttiple.txt and tetrad.txt respectively. =========================================== Changelog =========================================== Version 1.0 =========================================== Contact =========================================== Any questions, problems, bugs are welcom and should be dumped to Enfeng Qi <ef521@126.com>
