NUPARM-Plus
A Program for analyzing sequence dependent variations in nucleic acid (DNA & RNA) double helices

 NUPARM-Plus - DOWNLOADS:

NUPARM-Plus standalone version is GNU Fortran code that can be compiled using the latest GFORTRAN compilers.

If you wish to install the program, please read the instruction below.

Click here to download NUPARM-Plus source code.

Additionally,if interested in getting base-pair information of the structure, use BPFIND program, whcih is a fortran program that identifies basepairs details with classifications based on standard base-edges. BPFIND becomes more handy when the duplex contains Non-Waston-Crick basepairs. Output of BPFIND can directly be passed to NUPARM-Plus for geometric anlaysis of the structures.

Click here to download BPFIND source code.

Note:

Features and additionaly functionalities can be added on request. Please contact Prof. Dhananjay or Prof. Bansal with the request. The latest versions of NUPARM-Plus and BPFIND can also be downloaded from  http://www.saha.ac.in/biop/bioinformatics.html

 INSTALLATION:

The program is organized in a single Fortran program file with two header files. Uncompress "NUPARM-Plus.tar.gz" file.

The folder "NUPARM-Plus"  contains the following files.

  • NUPARM-Plus.f
  • parameters.h
  • coordinates.h
  • AdeVariants.name
  • CytVariants.name
  • GuaVariants.name
  • UraVariants.name

Program can be compiled by most of the available compilers, such as g77, g95, ifort, gfortran, etc. The program requires four files (AdeVariants.name, etc) containing names of different nucleotide variants. In the supplied code the program expects those files to be present in the current working directory.

gfortran NUPARM-Plus.f -o nuparm-plus

Questions or problems regarding this web site should be directed to [mb@mbu.iisc.ernet.in].
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