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Event Center
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1. Sequence Analysis
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2. Genomics 7
3. Systems Biology
4. Molecular Modelling Latest News
5. Bio-Live CD's  News
more
Navigation 6. Bio-Languages
 Articles

Upcoming Sequence Analysis:

events
 No
upcoming  
events available.

BioEdit TOP
more

BioEdit is a full integrated

Search sequence/alignment editor.
Performs translations, phylogenetic
analysis, clustalw alignments, ABI
trace analysis, RNA comparative
analysis and BLAST searches.

URL:http://www.mbio.ncsu.edu/BioEdit/b
ioedit.html

BLAST TOP

BLAST 2.0, (Basic Local Alignment

Search Tool), provides a method for
rapid searching of nucleotide and
protein databases.

URL:http://blast.ncbi.nlm.nih.gov/Blast.cg
i

BOXSHA
TOP
DE

BOXSHADE is a program for

creating good looking printouts
from multiple-aligned protein or
DNA sequences. The program does
no alignment by itself, it has to take
as input a file preprocessed by a
multiple alignment program or a
multiple file editor.

URL:ftp://www.isrec.isb-sib.ch/pub/
Circle TOP

Infer RNA secondary structure

using the comparative method.
URL:http://taxonomy.zoology.gla.ac.uk/ro
d/circles/

Clustal
W TOP

Clustal-W is a multiple sequence

alignment program. It provides an
integrated environment for
performing multiple sequence and
profile alignments and analyzing
the results.

URL:ftp://ftp.ebi.ac.uk/pub/software/uni
x/clustalw/

ClustalX TOP

ClustalX is a new windows interface

for the ClustalW. It provides an
integrated environment for
performing multiple sequence and
profile alignments and analyzing
the results.

URL:ftp://ftp.ebi.ac.uk/pub/software/dos
/clustalx/

Dambe TOP

It is a general-purpose package for

DNA and protein sequence
phylogenies, and also gene
frequencies.
URL:http://aix1.uottawa.ca/~xxia/softwa
re/software.htm
http://www.tigr.org/software/GlimmerH
MM/

Glimmer
M TOP

A gene finder derived from

Glimmer, but developed specifically
for eukaryotes. It is based on a
dynamic programming algorithm
that considers all combinations of
possible exons for inclusion in a
gene model and chooses the best of
these combinations. The decision
about what gene model is best is a
combination of the strength of the
splice sites and the score of the
exons generated by an interpolated
Markov model (IMM).

URL:
http://www.tigr.org/software/glimmerm/

MUMmer TOP

MUMmer is a system for rapidly

aligning entire genomes, whether in
complete or draft form.

URL:
http://www.tigr.org/software/mummer/

pDRAW TOP

pDRAW32 is being developed as a

free time hobby project. It is far
from finished, but as it has reached
a point where it could be helpful for
many labs, it is now available to the
scientific community.

URL:http://www.acaclone.com/
PrimerD
esign TOP

Primer Design is a DOS-program to

choose primer for PCR or
oligonucleotide probes. It is
tailored to check known sequences
for repeats and unique sequences
and subsequently to create prober
primers according to this data. A lot
of constrains are available to meet
your conditions. It can handle up to
32000 base pairs.

URL: http://www.bioinf-
club.com/software/

Sequin TOP

Sequin is a stand-alone software

tool developed by the NCBI for
submitting and updating entries to
the GenBank, EMBL, or DDBJ
sequence databases. It is capable
of handling simple submissions that
contain a single short mRNA
sequence, and complex submissions
containing long sequences, multiple
annotations, segmented sets of
DNA, or phylogenetic and
population studies.

URL:
http://www.ncbi.nlm.nih.gov/Sequin/

Staden TOP

The Staden Package consists of a

series of tools for DNA sequence
preparation (pregap4), assembly
(gap4), editing (gap4) and
DNA/protein sequence analysis
(spin).

URL: http://staden.sourceforge.net/
 

ADVICE TOP

Automated Detection and Validation

of Interaction by Co-Evolution
(ADVICE) takes a list of protein
sequences or sequence pairs as
input and uses orthologous
sequences to assess the similarity
in the evolutionary history of the
proteins. It is suggested that co-
evolution of proteins is useful for
predicting and validating protein-
protein interactions.

URL: http://advice.i2r.a-star.edu.sg/

ANTHEP
ROT TOP

ANTHEPROT (ANalyse THE

PROTeins) is to integrate into a
single package most of the methods
designed for protein sequence
analysis.

URL: http://antheprot-pbil.ibcp.fr/

CNplot TOP

CNplot is a network visualization

tool that can be used for large-scale
networks, as long as they are pre-
clustered.

URL:
http://csb.stanford.edu/~nbatada/VCN.ht
ml

Graphvi TOP
z

Graph layout software for protein

network.

URL: http://www.graphviz.org/

InterVie
wer TOP

InterWeaver is a tool employing

two approaches to detect potential
protein interactions by searching
for and interpreting evidence
available from on-line databases.
The first approach finds
homologues for a sequence and
searches for interacting partners in
protein interaction and literature
databases, and the second finds
sequence domains, and then
searches for domain fusion events
and possible domain interactions.

URL: http://wilab.inha.ac.kr/protein/

Osprey TOP

Application for graphically

representing physical and genetic
biological interactions; is coupled
with the General Repository of
Interaction Datasets (The GRID);
available for Unix and Windows.

URL:
http://biodata.mshri.on.ca/osprey/servlet
/Index

Pajek TOP

Program for Larger Network

Analysis.
URL: http://vlado.fmf.uni-
lj.si/pub/networks/pajek/default.htm

PIN TOP

To visualize the protein's

interaction and function
annotations. The software allows
the user to search for information
on putative protein interactions and
function classes.

URL: http://www.bioinfo.org.cn/PIN/

Teverna TOP

Taverna is a tool for creating and

running bioinformatics workflows.

URL: http://taverna.sourceforge.net/

WinPep TOP

A versatile tool for the analysis of

amino acid sequences.

URL:
http://www.ipw.agrl.ethz.ch/~lhennig/wi
npep.html

Systems Biology:

Cellwar
e TOP

Cellware has been designed to

conduct modeling and simulation of
gene regulatory and metabolic
pathways and also offer an
integrated environment for diverse
mathematical representations,
parameter estimation and
optimization. In addition, a user-
friendly graphical display and
capability to run large and complex
models would be provided by
default. A very special feature of
Cellware is that it would be the first
grid based modeling and simulation
tool in the field of Systems Biology.

URL: http://www.bii.a-
star.edu.sg/research/sbg/cellware/

CytoSca
pe TOP

Cytoscape is a visualization
platform for use with molecular
interaction networks. Interaction
data can be integrated with other
state data such as gene expression
profiles. The input to Cytoscape
includes lists of interaction pairs,
and tab/space delimited files
containing mRNA expression
profiles. The nodes of the
interaction networks can be filtered
by such variables as GO annotations
and number of interactions.

URL: http://www.cytoscape.org/

E-Cell 3 TOP

E-Cell Project is an international

research project aiming to model
and reconstruct biological
phenomena in silico, and
developing necessary theoretical
supports, technologies and
software platforms to allow precise
whole cell simulation.

URL: http://www.e-cell.org/
Gepasi TOP

Gepasi is a software package for

modeling biochemical systems. It
simulates the kinetics of systems of
biochemical reactions and provides
a number of tools to fit models to
data, optimize any function of the
model, perform metabolic control
analysis and linear stability
analysis.

URL: http://www.gepasi.org/

Molecular Modeling:

3D-Dock
Suite TOP

[FTDock, RPScore and MultiDock]

FTDock ( Fourier Transform Dock )

performs rigid-body docking on two
biomolecules in order to predict
their correct binding geometry.
FTDock outputs multiple
predictions that can be screened
using biochemical information.

URL: http://www.bmm.icnet.uk/docking/

ArgusLa
b TOP

It is an incredible molecular
modeling, graphics, and drug
design program.

URL: http://www.planaria-software.com/

Biodesig TOP
ner

It is a molecular modeling and

visualization program for personal
computers which is capable of
creating homologous models of
proteins, evaluate, and refine the
models.

URL:
http://www.pirx.com/biodesigner/index.s
html

Chem2P
ac TOP

Chem2Pac is intended to be a kind

of computational chemistry
integrator, which has a multiple
document interface, a molecular
rendering utility, and allows the
manipulation of various files.

URL:
http://www.ifi.unicamp.br/gsonm/chem2
pac/

Cn3D TOP

Cn3D is a helper application for

your web browser that allows you
to view 3-dimensional structures
from NCBI's Entrez retrieval
service.

URL:
http://ncbi.nih.gov/Structure/CN3D/cn3d
.shtml

Dang TOP

Dang reads coordinates from a

Protein DataBank (PDB) molecular
structure file and generates a table
of several useful geometric
measurements for each residue or
base. In its most basic form, it
writes out dihedral angles (phi, psi,
chi) hence the name. The output is
formatted for easy parsing by awk,
grep, sort and other UNIX utilities.

URL:
http://kinemage.biochem.duke.edu/softw
are/dang.php

DomainF
inder TOP

It is an interactive program for the

determination and characterization
of dynamical domains in proteins.
Its key features are computational
efficiency: even large proteins can
be analyzed using a desktop
computer in a few minutes ease of
use: a state-of-the-art graphical
user interface export of results for
visualization and further analysis
(VRML, PDB, and MMTK object
format).

URL: http://dirac.cnrs-
orleans.fr/DomainFinder/

Easy
Winbabe TOP
l

It's a program for chemists and

physicists dealing with molecular
modeling. It uses the well known
BABEL program as basis and
provides a windows interface. The
zip file includes BABEL ver 1.6.

URL:
http://users.uoi.gr/nkourkou/babel.html

EDPDB TOP
EdPDB is a program to manipulate
and extract information from
Brookhaven Protein Databank
(PDB) format coordinate file(s) of
three-dimensional protein
structures.

URL:
http://omega.omrf.ouhsc.edu/zhangc/ed
pdb/edpdb.html

Garlic TOP

It is a free molecular visualization

program, protein structure, DNA
structure, PDB, molecular
rendering, biological
macromolecule, unix, linux, free
software download, open source
software.

URL: http://garlic.mefos.hr/garlic-1.0/

Ghemical TOP

Ghemical is a computational
chemistry software package
released under the GNU GPL.
Geometry optimization, molecular
dynamics and some visualization
tools are currently available. If
quantum-mechanical calculations
are needed, Ghemical can be
directly linked into the quantum
chemistry program MPQC (which is
also distributed under GNU GPL).
Therefore Ghemical can serve as a
graphical front-end for the MPQC
program, currently providing
various 3D-plots for electron
densities, molecular orbitals and
molecular orbital densities.

URL:
http://www.uku.fi/~thassine/ghemical/
gOpenM
ol TOP

gOpenMol graphics interface to the

OpenMol and can be used for the
analysis and display of molecular
dynamics trajectories and the
display of molecular orbital's,
electron densities and electrostatic
potentials.

URL: http://www.csc.fi/gopenmol/

GRAMM TOP

GRAMM is a program for protein

docking. To predict the structure of
a complex, it requires only the
atomic coordinates of the two
molecules (no information about
the binding sites is needed). The
program performs an exhaustive 6-
dimensional search through the
relative translations and rotations
of the molecules. The molecular
pairs may be: two proteins, a
protein and a smaller compound,
two transmembrane helices, etc.
GRAMM may be used for high-
resolution molecules, for inaccurate
structures (where only the gross
structural features are known), in
cases of large conformational
changes, etc.

URL:
http://www.chem.ac.ru/Chemistry/Soft/
GRAMM.en.html

GROMAC
S TOP

GROMACS is a versatile package to

perform molecular dynamics, i.e.
simulate the Newtonian equations
of motion for systems with
hundreds to millions of particles.
URL: http://www.gromacs.org/

HEX TOP

Hex is an interactive protein

docking and molecular
superposition program. Currently,
Hex understands protein and DNA
structures in PDB format.  <!--[if !
supportLineBreakNewLine]-->
<!--[endif]-->

URL: http://www.csd.abdn.ac.uk/hex/

KineMag
e TOP

A "kinemage" (kinetic image) is a

scientific illustration presented as
an interactive computer display.
Operations on the displayed
kinemage respond immediately: the
entire image can be rotated in real
time, parts of the display can be
turned on or off, points can be
identified by selecting them, and
the change between different forms
can be animated.

URL:
http://kinemage.biochem.duke.edu/kinem
age/magepage.php

LOOPP TOP

LOOPP is a fold recognition

program based on the collection of
numerous signals, merging them
into a single score, and generating
atomic coordinates based on an
alignment into a homologue
template structure.

URL:
http://cbsu.tc.cornell.edu/software/loopp
/index.htm

MOIL TOP

MOIL is a molecular modeling

software, which is in the public
domain, and is written in the group
of Ron Elber. Available features,
such as energy calculations,
minimization and calculations of
classical trajectories. Graphic User
Interface for a wide range of moil
applications on a Windows desktop.
This interface enables direct
calculation on a desktop, on a
Windows cluster, and on properly
configured web servers.

URL:
http://cbsu.tc.cornell.edu/software/moil/
moil.html

MOLMOL TOP

MOLMOL is a molecular graphics

program for displaying, analyzing,
and manipulating the three-
dimensional structure of biological
macromolecules, with special
emphasis on the study of protein or
DNA structures determined by NMR.

URL:
http://hugin.ethz.ch/wuthrich/software/
molmol/

Molscript TOP

A program for displaying molecular

3D structures, such as proteins, in
both schematic and detailed
representations.

URL: http://www.avatar.se/molscript/
NAMD TOP

NAMD, recipient of a 2002 Gordon

Bell Award, is a parallel molecular
dynamics code designed for high-
performance simulation of large
biomolecular systems. Based on
Charm++ parallel objects, NAMD
scales to hundreds of processors on
high-end parallel platforms and
tens of processors on commodity
clusters using gigabit ethernet.
NAMD is file-compatible with
AMBER, CHARMM, and X-PLOR and
is distributed free of charge with
source code.

URL:
http://www.ks.uiuc.edu/Research/namd/

NOC TOP

It is a free program for protein

structure model-building,
visualization, validation and
analysis.

URL: http://noc.ibp.ac.cn/

OpenBab
le TOP

Open Babel is a project designed to

pick up where Babel left off, as a
cross-platform program and library
designed to interconvert between
many file formats used in molecular
modeling and computational
chemistry.

URL: http://openbabel.sourceforge.net/
Rasmol TOP

Rasmol is a molecular graphics

program intended for the
visualization of proteins, nucleic
acids and small molecules.

URL:
http://www.umass.edu/microbio/rasmol/
index2.htm

Raster
3D TOP

Raster3D is a set of tools for

generating high quality raster
images of proteins or other
molecules. The core program
renders spheres, triangles,
cylinders, and quadric surfaces with
specular highlighting, Phong
shading, and shadowing. It uses an
efficient software Z-buffer
algorithm which is independent of
any graphics hardware.

URL:
http://www.bmsc.washington.edu/raster
3d/raster3d.html

Reduce TOP

Reduce is a program for adding

hydrogens to a Protein Data Bank
(PDB) molecular structure file.
Hydrogens are added in
standardized geometry with
optimization of the orientations of
OH, SH, NH3+, Met methyls, Asn
and Gln sidechain amides, and His
rings. Both proteins and nucleic
acids can be processed. HET groups
can also be processed as long as
the atom connectivity is provided. A
slightly modified version of the
connectivity table published by the
PDB is included
(reduce_het_dict.txt).

URL:
http://kinemage.biochem.duke.edu/softw
are/reduce.php

SPDBVie
wer TOP

Swiss-PdbViewer is an application
that provides a user friendly
interface allowing to analyze
several proteins at the same time.
The proteins can be superimposed
in order to deduce structural
alignments and compare their
active sites or any other relevant
parts. Amino acid mutations, H-
bonds, angles and distances
between atoms are easy to obtain
thanks to the intuitive graphic and
menu interface.

URL: http://au.expasy.org/spdbv/

TraX TOP

TraX (Trajectory eXplorer) is a

simple Biodesigner-like program
working under Linux and Windows.
The program allows reading a
protein folding simulation
trajectory (TRA file) and saving a
single frame as a PDB file.

URL:
http://www.pirx.com/biodesigner/downlo
ad.html

VEGA TOP

VEGA was originally developed to

create a bridge between most of
the molecular software packages
only, but in the years, enhancing its
features, it's evolved to a complete
molecular modeling suite.

URL: http://users.unimi.it/~ddl/

BioKnop
pix TOP

Bioknoppix is a customized
distribution of Knoppix Linux Live
CD. With this distribution you just
boot from the CD and you have a
fully functional Linux OS
distribution with open source
applications targeted for the
molecular biologist. Beside using
some RAM, Bioknoppix doesn't
touch the host computer, being
ideal for demonstrations, molecular
biology students, workshops, etc.

URL: http://bioknoppix.hpcf.upr.edu/

BLAST-
Server TOP

A BLAST server ready to run. Just

pop the CD, boot the computer and
you have a BLAST server . BLAST is
one of the most useful
bioinformatics application.

URL:
http://www.genesdigitales.com/blastoncd
/
DNA
Linux TOP

DNALinux is a Linux distribution

with bioinformatics software pre-
installed. DNA and protein
sequence manipulation software is
included. Like EMBOSS, Primer3,
ClustalW, T-Coffe and others.

URL: http://www.dnalinux.com/

Vigyaan TOP

Vigyaan is an electronic workbench

for bioinformatics, computational
biology and computational
chemistry. It has been designed to
meet the needs of both beginners
and experts. VigyaanCD is a live
Linux CD containing all the required
software to boot the computer with
ready to use modeling software.

URL: http://www.vigyaancd.org/

V-Linux TOP

VLinux Bioinformatics workbench is

a Linux distribution for
Bioinformatics. It is easy to use, no
installation required, CD-based
distribution based on Knoppix 3.3.
It includes a variety of sequence
and structure analysis packages.

URL:
http://bioinformatics.org/vlinux/index.ph

Bio-Languages:

BioJava TOP

BioJava is an open-source project

dedicated to providing a Java
framework for processing biological
data. It include objects for
manipulating sequences, file
parsers, DAS client and server
suport, access to BioSQL and
Ensembl databases, and powerful
analysis and statistical routines
including a dynamic programming
toolkit.

URL: http://www.biojava.org/

BioMOB
Y TOP

An international group of biological

data hosts, biological data service
providers, and coders whose aim is
to set standards for biological data
representation, distribution, and
discovery.

URL: http://biomoby.org/

BioPerl TOP

Bioperl is a collection of perl

modules that facilitate the
development of perl scripts for
bioinformatics applications. As
such, it does not include ready to
use programs in the sense that
many commercial packages and
free web-based interfaces do (e.g.
Entrez, SRS). On the other hand,
bioperl does provide reusable perl
modules that facilitate writing perl
scripts for sequence manipulation,
accessing of databases using a
range of data formats and
execution and parsing of the results
of various molecular biology
programs including Blast, clustalw,
TCoffee, genscan, ESTscan and
HMMER. Consequently, bioperl
enables developing scripts that can
analyze large quantities of
sequence data in ways that are
typically difficult or impossible with
web based systems.

URL: http://bio.perl.org/

BioPipe TOP

The biopipe is a workflow

framework that seeks to address
some of the complexity involved in
carrying out large scale
bioinformatics analysis. It has been
designed to work intimately with
the bioperl package. The main idea
behind biopipe is to enable users to
integrate data from disparate
sources into a common analysis
framework. In addition, it is
designed to work over a compute
farm providing job management
functionality. This project was
extended borrowing code and
concepts from the Ensembl pipeline
project.

URL: http://biopipe.org/

BioPyth
on TOP

An international association of
developers of freely available
Python tools for computational
molecular biology. biopython.org
provides an online resource for
modules, scripts, and web links for
developers of Python based
software for life science research.

URL: http://www.biopython.org/

BioRuby TOP
 BioRuby project aims to implement
an integrated environment for
Bioinformatics with Ruby language.
The BioRuby library follows the
KISS principle in order to maximize
its usability and efficiency for
biologists as a daily tool.

URL: http://bioruby.org

Bio-LiveCDs
Proteomics:

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