In-House Software Development Activity
To help the users from time to time, algorithms and programs are developed in the areas such as taxonomic classification, sequence analysis and structure prediction. A package for the production division of plant tissue culture industry is being developed. Similarly, general purpose programs for sequence analysis and molecular visualisation are developed in collaboration with the Centre for Development of Advanced Computing (C-DAC). These are PRAS, PNAS and MG which are marketed by C-DAC. Twenty copies of each of these programs are sold to various Universities and Research Institutions. Both the DOS and the transputer versions of these packages are available. It may be mentioned here that PRAS has received the BEST APPLICATION AWARD - "PARAM" instituted by C-DAC.
PRAS (Parallel Multiple Sequence Alignment Package)
There are three main computational modules viz. pairwise alignments of sequences, cluster analysis, profiling and collapsing of sequences. DOS version can simultaneously align 10 sequences upto 1000 characters each and the transputer version can align 100 sequences of 1000 characters.
The data and algorithmic parallelization is carried out efficiently to get almost a linear gain with an increase in the number of transputers. This is the first ever application of parallel processing to the multiple sequence alignment problem in the world.
PNAS (Protein and Nucleic Acid query System)
The PNAS allows analysis of protein and nucleic acid sequence data. This is a user-friendly package written in C and has all features that are available in most commercial packages. In addition, PNAS has several routines based on the methods developed in-house to analyse the sequence data.
MG (Molecular Graphics)
This is the first Indian molecular visualization package that runs on the IBM compatible system. It allows the visualization of the molecules as ball and stick, ribbon and CPK in an user-friendly environment. It allows the manipulation of the molecules through rotation, zoom-in and out, calculation of geometrical parameters, protein and nucleic acid molecules can be built from its sequence information.
MX - Molecular graphics and analysis software is an open ended molecular modelling software based on X - windows. This program displays molecules in wireframe, ball and stick, backbone and depth qued sphere representations. Graphics operations like rotation, translation, zooming, front and back clipping of the screen image is possible. The program also calculates all internal parameters of a molecule. For proteins (f ,Y ) angles are calculated and displayed in a Ramachandran plot. Other functions include an interface to secondary structure analysis program DSSP and a method based on Ca –Ca distance criteria developed in-house to decide the accuracy of predicted protein structure. The program can also help in creation of constraints file required for molecular simulations using AMBER. An energy minimizer that uses genetic algorithm is also available and that can be plugged in.
X-windows based program to view nucleic acid molecular dynamics results in 'Dials and Windows' format. The program accepts pre-processed data from structure analysis programs like CURVES and generates dials and windows plots for their visualisation.
The program also gives two dimensional pseudo colour views of rms deviations.
Genetic Algorithms for Structure Prediction
To predict three-dimensional structure of proteins and nucleic acids from their sequences, program based on Genetic Algorithms is being developed. This program is parallelised to obtain better efficiency, and works in PVM environment on the new PARAM system of C-DAC.
Parallel AMBER and CHARMM on PARAM Open Frame
AMBER - Assisted Model Building with Energy Refinement program is widely used to carry out molecular dynamics studies of biopolymers in general and oligonucleotides in particular. Molecular Dynamics (MD) studies being compute intensive, molecules of biological interests are difficult to study even today. To overcome this hurdle the parallel version of AMBER was ported on the Indian Supercomputer PARAM Open Frame. The code which uses the farm field topology and dynamic load balancing, gave better benchmarking results on PARAM Open Frame with only eight nodes, than SPP (Scripps), SP2 (Cornell), T3D (Pittsburgh) and Cray-T90. This program was then used to carry out unconstrained MD studies on duplex of 13-mer oligonucleotide substrate of Pvull with the aim to gain an insight in the problem of mechanism of recognition and cleavage by type II endonucleases of DNA. MD studies, with only Watson-Crick base pairing constraint, were carried by immersing it in the water for 1 nano second at 283 k. Later simulations are also carried out for the same molecule in water with Na+ ions for 1.3 nano second at 283 k. To our knowledge such large simulations are not carried out anywhere in the world. Similarly, CHARMM- Chemistry at HARvard Molecular Mechanics is ported on parallel machine PARAM open frame. This work is carried out in collaboration with C-DAC.
The first multimedia teaching-aid package in life sciences from India has been developed at our Centre on the "Immune System". The package is based on the windows environment using the Asymetrix Toolbook as the authoring software. The softwares like 3D studio, Animator Pro, CorelDraw, Photopoint video edit were also used to process images and animations. The present module of the package covers the overview of the immune system with a stress on fundamentals of immunology.
CURVES : Structural analysis of nucleic acids
InSight II (Biosym) : Ampac/Mopac, Biopolymer, Builder, DelPhi,Discover, DMol, Viewer modules
JUMNA : Building and minimization of nucleic acids
NAMOT : Modelling of nucleic acids
X-PLOR : A system for X-ray crystallography and NMR
AMBER : Molecular Modelling with energy minimization routines and dynamics
MX : X-windows based graphics and analysis program
MxCurv : X-windows based graphics program to view Nucleic acid dynamics results in 'Dials & windows' format
SOPM : Consensus secondary structure prediction using the available prediction methods
NAMD : Parallel program for molecular dynamics
Parallel AMBER : Parallel version of AMBER
CHARMM : Parallel version of CHARMM
DTMM : DeskTop Molecular Modeller
MG : Molecular Graphics package :
PCM : PC Modeller
RASMOL : Molecular modelling package
Sequence Analysis Programs
Homology(Biosym) : Three dimensional structural homology program
AMPS : Multiple Alignment of Sequences package
BLA : to search motifs from BLAST searches
CAP : Consistent Alignment Parser
CINEMA : Colour INteractive Editor for Multiple Alignments
CLUSTALW : Multiple Alignemnt software package
EMBL2NBRF : Sequence Format Converter
FASTA : Fast sequence homology search program.
READSEQ : Sequence Format Converter
PC BASED/WINDOWS/NT BASED
ANTHEPROT : Protein Sequence and Circular Dichroism analysis
ANTIGEN : Predicts the antigenic sites
AUTHORIN : Sequence data submission software
DNASTAR : Sequence analysis software
GENEDOC : Multiple sequence alignment editor and shading utility
MACAW : Multiple Alignment Construction and Analysis Workbench
MEGA : Molecular Evolutionary Genetic Analysis
PAPA : To generate PArsimony trees after Progressive Alignment
PHYLIP : Phylogeny Inference Package
PNAS : Protein and Nucleic Acid query System
PRAS : Multiple PaRAllel Sequence alignment package
TPRAS : Transputer version of PRAS
PSQ : Protein Sequence Query program
SEQAID : Sequence analysis
SEQUIN : GenBank Sequence submission
VISED : Visual sequence editor
AVIS : Animal Virus classification
BACTERIAL : Probabilistic Identification package for
DELTA : Software for taxonomy
FREAK : Matrix generation program for probabilistic identification
MICRO-IS : Database management system for micro-organisms
TAXAN : Package for cluster analysis
TREEVIEW : Phylogenetic trees from alignment files
CLUE : Statistical cluster analysis package
IDAMS : UNESCO's Internationally Developed data Analysis and Management package
PCCALC : Spread sheet
Teaching Aid Packages
GROLIER : Encyclopaedia on CDROM
Immunology : Multimedia tutor for Immune System
SPEED : World's first interactive teaching aid movie on CDROM
Gene Cloning and Sequencing
Geneism Simulation of experiments in Genetics
Genetics and Protein Synthesis
Protein Sequence Apprentice
Protein Structure Enzyme Activity
Subcellular Fraction and Centrifugation
ClinPharm 1.5 : Predicts the effects of clinical conditions on pharmacokinetics of drugs.
MACDOPE : Model of Human pharmaco kinetics
MACEE : Model of body fluids and electrolyte
MACMAN : A simulation of heart, circulation, kidneys, body fluids and hormones
MACPEE : A simulation of heart peripheral circulation and arterial baroreceptor function
MACPUF : A simulation of human respiration, gas exchange and control
Instructor : A tutor for IBM PCs and compatibles
DBMS tutor : Tutor for Data Base Management Systems
Professor : PC tutor
Microcomputers In Biology