
 ======================= 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 directories 'sipris1.0', which 
contains several subdirectories, and 'alignments'.  

 --------------------- 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.

The alignments directory contains the input multiple sequence alignments (in cma 
format) used for BPPS analyses and the BPPS-generated contrast alignments corresponding
to the SIPRIS analyses.

 ******************************************************************************************
    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
 ******************************************************************************************

