NAME
BPNet
SYNOPSIS
bpnet.linux [OPTIONS] [FILE...]
DESCRIPTION
This program is for calculating the overlap between
two bases in a nucluic acid for RNA. The output is
stored in a .rob file with the same name of the .cor
file name.
INSTLLATION
EASY-METHOD
Download the binary executable 'bpnet.linux' and place it to some suitable folder.
Done.
HARD-METHOD
If that does not work for you for any reason, then download the src folder
and compile the same following the instructions given below.
COMPILE:
cd src
make clean
make
Then move the binary executable 'bpnet.linux' to your suitable path.
SETUP
BPNet uses several files for its work. These are kept in 'sysfiles' directory.
copy all of them and paste them in a folder. We prefer the following.
/usr/local/bin
PATH-SETTING
BPNet reads system files through an environment variable called NUCLEIC_ACID_DIR.
Suppose you have put all the files of 'sysfiles' directory in the /usr/local/bin,
then put the following line in your '.bashrc' file.
export NUCLEIC_ACID_DIR=/usr/local/bin/
PARALLEL-MODE
BPNet can run in parallel mode. But for this OpenMP library should be installed
in your machine.
PARALLEL-MODE COMPILE
cd src
make clean
make -f Makefileprll
PARALLEL-MODE SETUP
In parallel mode, you have to do all the setup and path settings
of the serial mode. In addition you have to set the OpenMP
environment variable. If our machine has 4 cores and each having
4 hyperthreads, i.e. 2x4 = 8 cpu. Then to achieve maximum from
the system, set the path as,
export OMP_NUM_THREADS=8
RUN
To run the program, go to the directory where the structure files are stored.
Then run as follows.
bpnet.linux xxxx.cif
INPUT
BPNet accepts mmCIF and PDB file formats.
OUTPUT
A full list of output files are listed below.
xxxx_rna.pdb
This file stores the RNA part only in PDB format.
xxxx.out
This file stores all the base-pair information.
xxxx.adj
It stores the adjacency information.
xxxx.fasta
This file stores the nucleic acid primary sequence in fasta format.
xxxx.dbn
This file is the base pair information in dot-bracket notation.
xxxx.bpseq
This file is the base pair information in bpseq notation.
xxxx.dat
This file stores the secondary structure information in fasta format.
The sequence here will look like, HHHHCCLLL, in this way. Here H means
the corresponding base is in helix, C represent that the residue is in
Coil, L Stands for Loop etc.
xxxx.hlx
This files stores the helix, loop and pseudo helix information.
xxxx_rna.pml
This one is to visualize the networks in RNA part only.
xxxx_cif.pml
This file is to visualize the same on the entire mmCIF file's context.
This program is an applet file ready for visualization using VARNA [Ref??] software.
This file stores all helix information.
A postscript file is generated to visualize the base base interaction.
The program also generates two secondary structure file namely dbn and bpseq file.
xxxx.ps
A postscript file to show the contact-map distribution.
xxxx_helix.pml
To visualize the networks in the context of other functional units like base pairs,
helix, loops etc.
xxxx.html
An applet file is generated to visualize the secondary structures in a better way.
The applet is compatible with VARNA (http://varna.lri.fr).
RUNTIME OPTIONS
BPNet uses several command line options to tune the result. The lollowing are the full lists
of the same.
GENERAL OPTIONS
--help
Shows a small help on terminal.
--pub
Prints the citation details of BPNet.
--genhelp
Generates this help.md file in the current directory.
--version
Prints the version of the program.
-nettype=[basepair/contact]
This option indicates base pair or contact based network.
Default is 'contact' based network.
EXAMPLE
bpnet.linux xxxx.cif -nettype=basepair
-netzise=from-to or -netsize=size
This option generates the network of the mentioned size.
default is 3-999999.
EXAMPLE
bpnet.linux xxxx.cif -netsize=4-5
bpnet.linux xxxx.cif -netsize=3
-exdeg=number
This option generates all the network which contains at least
one vertex with degree 'count'. 'exdeg' means 'exists degree'.
EXAMPLE
bpnet.linux xxxx.cif -exdeg=3
-numexdeg=number
This one considers those networks where the total nodes with specific
degree is required.
EXAMPLE
bpnet.linux xxxx.cif -exdeg=3 -numexdeg=2
-cycles=number
This option generates the networks where there is at least two cycles.
EXAMPLE
bpnet.linux xxxx.cif -cycles=2
-wttype=[c1p-c1p]
Default BPNet considers E-val (Ref: https://doi.org/10.1080/07391102.2006.10507108)
for base pairs and surface overlap for contact based network. But these can be changed
to C1'-C1' distance.
EXAMPLE
bpnet.linux xxxx.cif -wttype=c1p-c1p
bpnet.linux xxxx.cif -wttype=c1p-c1p -nettype= basepair
-wtcutoff=value
Default the contact based network considers any bases whose surface
contact greater than 0. But the user bay change it to a desired positive
value. In that case all contacts greater ot equal to that value will be
considered for contact based network.
EXAMPLE
bpnet.linux xxxx.cif -wtcutoff=10.0
BASEPAIR RELATED OPTIONS
BPNet accepts several options for base pair generations.
-hbdist=value
BPNet program uses 3.8A as the default distance of donor-acceptor
atoms for Hydrogen bond. User may change the same using this option.
EXAMPLE
bpnet.linux xxxx.cif -bhdist=4.2
-sugmed=[true/false]
BPNet by default considers O2' atom of sugar-phosphate backbone for sugar
mediated base pairs. If the user does not want that, then they can set it
to 'false'
EXAMPLE
bpnet.linux xxxx.cif -sugmed=false
-chmed=[true/false]
By default BPNet considers C-H...O/N mediated H-bonds for base pairs. It one
wants to exclude them then they can choose it as false.
EXAMPLE
bpnet.linux xxxx.cif -chgmed=false
-hetatm=[true/false]
By default BPNet considers all modified nucleobases. If the user wants
to exclude them, then they can do so by this option.
EXAMPLE
bpnet.linux xxxx.cif -hetatm=false
-chain=name
If one supply the chain name, the program computes network on the
mentioned chain.
CAUTION !!!
If a chain is selected then the program only sees that chain.
So, if a base of the given chain has a network with the bases
of the other chain, the program will not report that.
EXAMPLE
bpnet.linux xxxx.cif -chain=A
ABBREVIATIONS
BASE PAIR EDGE
W - Watson-Crick edge (Capital W).
H - Hoogsteen edge (Capital H).
S - Sugar edge (Capital S).
w - Watson-Crick edge with one or more C-H...O/N type of hydrogen bond (Small w).
h - Hoogsteen edge with one or more C-H...O/N type of hydrogen bond (Small h).
s - Sugar edge with one or more C-H...O/N type of hydrogen bond (Small s).
+ - Protonated Watson-Crick edge.
z - Protonated Sugar edge.
g - Protonated Hoogsteen edge (rarely found though).
ORIENTATION
C - Cis Orientation.
T - Trans Orientation.
PAIR TYPE
BP - Normal base pair.
TP - Tartiary pair.
BF - Bifurcated pair (Follow our paper BPFIND(2006) )
BUG REPORT
Email bug reports to the bug-reporting address
⟨roy.parthajit@gmail.com⟩ or
⟨dhananjay.bhattacharyya@saha.ac.in⟩