======================= BPPS-SIPRIS Main README file ========================== Extract executables and other files by first typing "gunzip sipris1.0.tar.gz" and then "tar xvf sipris1.0.tar" This will create the directory 'sipris1.0', which contains several subdirectories. --------------------- Sample BPPS-SIPRIS analysis ---------------------- To perform a complete (start to finish) BPPS-SIPRIS analysis of Frizzed domain proteins go into the 'complete_run/' subdirectory and type './run '. This illustates the steps required to similarly analyze other protein domains. This should take about an hour to finish. ------------------------------------------------------------------------ The 'bin' subdirectory contains the programs needed to perform BPPS-SIPRIS analysis, namely fatax, MAPGAPS, BPPS and SIPRIS. These executables were compiled under a RedHat 5.9 Linux operating system (kernelrelease 2.6.18-371.1.2.el5) running on an Intel Xeon x86_64 machine. fatax adds phylum annotations to fasta formatted sequences in the NCBI non-redundant (nr) database. Type './bin/fatax - ' for usage and how to obtain the taxonomy input files. The MAPGAPS program creates a large multiple sequence alignment (MSA) required as input to the BPPS program. Type './bin/mapgaps ' for usage. See README.mapgaps for details. The BPPS program identifies hierarchically-arranged subgroups within a protein superfamily based on correlated residue patterns distinctive of each subgroup. Type './bin/bpps ' for usage. See README.bpps for details. The SIPRIS program finds statistically significant networks of structurally interacting pattern residues. SIPRIS also requires the programs PyMol (http://www.pymol.org) and Reduce (http://kinemage.biochem.duke.edu/software/reduce.php). Type './bin/sipris ' for usage. See README.sipris for details. ****************************************************************************************** Copyright (C) 2017 Andrew F. Neuwald, The University of Maryland School of Medicine. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHOR OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. For further information contact: Andrew F. Neuwald Institute for Genome Sciences and Department of Biochemistry & Molecular Biology University of Maryland School of Medicine 801 West Baltimore St. BioPark II, Room 617 Baltimore, MD 21201 Tel: 410-706-6724; E-mail: aneuwald@som.umaryland.edu ******************************************************************************************