Create README.md

README.md

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+BPFind v. 1.8
+(http://www.saha.ac.in/biop/dhananjay.bhattacharyya/bpfind.tar.gz)
+
+Please cite the reference while using BPFind tool:
+
+Non-canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal 
+Structure Database Analysis(2006), 
+Das, J.; Mukherjee, S.; Mitra, A.; Bhattacharyya, D., J. Biomol. Struct. Dynam.,
+24,149.
+
+
+(For any query, please mail to: dhananjay.bhattacharyya@saha.ac.in)
+
+
+BPFind is a software tool for detecting stable and feasible basepairs present in
+nucleic acid molecules. It finds potential H-bonds within the molecule and 
+checks for the basepair geometry to output the best possible pairing pattern 
+between a pair of bases. BPFind considers both the standard N/O-H...N/O and
+non-polar C-H...O/N types of hydrogen bonding.  However, one can also detect
+those basepairs stabilized only by regular polar hydrogen bonds.
+
+
+1. Input File Type:
+-------------------
+
+Files containing coordinates of the atoms in PDB format (XXXX.pdb). 
+
+2. Output File Description:
+---------------------------
+
+XXXX.cor - Contains coordinates of the nucleic acids only considered for 
+           searching H-bonds. Base moieties, not having all the 
+           purine/pyrimidine ring atoms and C1' atoms, are not considered for 
+           basepairing. Therefore, they are not included in XXXX.cor files.
+XXXX.out - Contains detailed descriptions of the basepairing patterns present 
+           within the RNA molecule.Format is as below:
+XXXX.nup - Contains basepairing information required to run the associated
+           basepair parameter calculation program NUPARM.  The NUPARM software
+           can also be downloaded from the same site.
+XXXX.dat - Contains base pairing information of each nucleotide residue in 
+           symple format, such as H for Watson-Crick basepairs, N for non-
+	   canonical basepairs, T for base triples and L for nonpaired bases
+XXXX.hlx - Contains base pairing information of only the double helices, 
+           ignoring the unpaired as well as isolated pairs.
+
+The XXXX.out file gives the basepairing informations in the following way:
+================================================================================
+Column starting from '>' mark represent the following:
+>Serial number of nucleotides
+----->Residue number as in PDB
+---------->Residue name
+--------------->Chain ID
+---------------->Serial number of the paired base
+--------------------->Residue number of the paired base as in PDB
+-------------------------->Residue name of the paired base
+------------------------------->Chain ID of the paired base
+--------------------------------->Base pair type
+-------------------------------------->Base pair indicator
+--------------------------------------->E-value indicating base pair deformation
+------------------------------------------->Equivalent info for other pairs
+================================================================================
+
+XXXX.fasta - Contains sequence of the nucleotide chains in a PDB file with 
+             residues having coordinates of all ring atoms and C1' atom.
+
+XXXX.hlx - Contains the pseudo-continuous stack regions in the nucleic acid
+           molecule as given by their BPFind numbering.
+
+
+
+3. Abbreviations Used in Output Files:
+--------------------------------------
+
+W - Watson-Crick edge
+H - Hoogsteen edge
+S - Sugar edge
+w - Watson-Crick edge with one or more C-H...O/N type of hydrogen bond
+h - Hoogsteen edge with one or more C-H...O/N type of hydrogen bond
+s - Sugar edge with one or more C-H...O/N type of hydrogen bond
++ - Protonated Watson-Crick edge
+z - Protonated Sugar edge
+C - Cis
+T - Trans
+
+
+4. Runtime Options:
+-------------------
+
+USAGE: BPFIND -[options] filename
+
+The following options can be used:
+-HD [value] to set default hydrogen bond distance cutoff (default = 3.8)
+-VA [value] to set default pseudo angle cutoff (default = 120.0)
+-EN [value] to set default E-value cutoff (default = 1.8)
+-HT to include HETATM entries in PDB
+-CH to avoid identification of base pairs stabilized by C-H...O/N H-bonds
+-SG to avoid identification of base pairs involving sugar O2' atoms
+-AB to avoid base pairing between residue no. i and i+1
+-OL to avoid printing base pairing information w.r.t.the second strand.  
+ This is suitable for simple oligonucleotides
+-ML [character] to detect base pairing within a particular selected chain of DNA/RNA
+-NMR to calculate base pairing information for the first model in NMR derived
+ensemble of structures
+
+5. Basepairing Criteria:
+------------------------
+
+BPFind maintains a few criteria for detecting basepairs:
+
+(i)   Bases not having coordinates of all the ring atoms (purine/pyrimidine) and
+      C1' atoms are not considered for detecting hydrogen bonds.
+(ii)  At least two hydrogen bonds must exist between two bases, at least one of
+      which must be between the base moieties. Basepairs involving both 2'-OH 
+      mediated hydrogen bonds are not detected by BPFind. It considers basepairs
+      for which both the H-bonds are of C-H...O/N type, as long as one H-bond is
+      found between the base rings.
+(iii) BPFind considers a range of modified bases which are usually under the 
+      'HETATM' lines in a PDB file. They are listed in the four files:
+      AdeVariants.name 
+      Guavariants.name
+      CytVariants.name
+      UraVariants.name
+      We keep these files in /usr/local/bin directory and the program also
+      expects them there.  In case you want to keep them somewhere else,
+      please modify the code (line nos. 57, 65, 73 and 81) to indicate the
+      location of these files.
+      Any new modified residue name can be included in one of these files 
+      accordingly in order to be recognized by  BPFind.
+(iv)  BPFind uses a cutoff distance of 3.8 angstrom between the acceptor and 
+      donor atoms, a cutoff angle of 120.0 degree for checking planarity of 
+      precursor atoms (designed carefully to accommodate more labile basepairs) 
+      and a cutoff E-value of 1.8 to signify the overall distortion and maintain
+      a good basepairing geometry.
+(v)   BPFind uses a more stringent option for protonated basepair options in 
+      order to avoid false positives. It considers cutoff angle of 150.0 degree
+      for protonated basepairs.
+(vi)  BPFind allows more flexibility if 2'-OH of the ribose sugar moiety is 
+      involved in hydrogen bonding - a cutoff angle of 100.0 degree.