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Holy Cross College
Sponsored by DBT.BTIS,
Ministry of Science & Technology, Govt. of INDIA |
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Holy Cross College
Sponsored by DBT.BTIS,
Ministry of Science & Technology, Govt. of INDIA |
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Department of Biotechnology and Bioinformatics
Circle
Infer RNA secondary structure using the comparative method.
URL: http://taxonomy.zoology.gla.ac.uk/rod/circles/
ClustalW
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: http://www.ebi.ac.uk/pub/software/unix/clustalw/
ClustalX
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: http://www.ebi.ac.uk/pub/software/dos/clustalx/
Dambe Windows
It is a general-purpose package for DNA and protein sequence phylogenies, and also gene frequencies.
URL: http://aix1.uottawa.ca/~xxia/software/software.htm
DCSE
DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment.
URL: http://rrna.uia.ac.be/dcse/
DNA
DNATools is a comprehensive program package for routine handling and analysis of nucleotide and protein sequences. The program includes functions for batch renaming, editing and annotating sequences, restriction mapping, translation, automated blast search and information retrieval, codon analysis, primer design and ordering and a lot more...
URL: http://www.crc.dk/dnatools/
DNA Club
PC program for Integrated analysis on DNA sequences.
URL: http://softwareseek.progenote.net/downloads/
Emboss
EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis.
URL: http://emboss.sourceforge.net/
FastA
The FastA program has been developed by Pearson & Lipman (1988) and is useful to find all protein sequences of a database such as Swiss-Prot, that are homologous to a given sequence.
URL: http://www.ebi.ac.uk/fasta33/
GeneDoc
GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
URL: http://www.psc.edu/biomed/genedoc/
Hmmer
A profile hidden Markov model that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
URL: http://hmmer.wustl.edu/
HyPhy
It intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more...
URL: http://www.hyphy.org/
JalView
Graphical multiple alignment editor. Requires Java Virtual Machine.
URL: http://www.jalview.org/
Jemboss
Jemboss is developed by the EMBOSS team. The software is free and part of the EMBOSS distribution.
URL: http://emboss.sourceforge.net/Jemboss/
Mega3
MEGA is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
URL: http://www.megasoftware.net/
MFold
Mfold is an RNA and DNA folding package.
URL: http://www.bioinfo.rpi.edu/~zukerm/export/mfold-3.html
NCBI ToolKit
The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.
URL: http://www.ncbi.nih.gov/toolbox/ncbi_tools/
PeptideMass
The Program cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest
URL: http://www.expasy.ch/tools/peptide-mass.html
RNA DRAW
It is an integrated program for RNA secondary structure calculation and analysis.
URL: http://www.rnadraw.com/
Readseq
Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.
URL: http://iubio.bio.indiana.edu/soft/molbio/readseq/
Seaview
SeaView is a graphical multiple sequence alignment editor. It is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.
URL: http://pbil.univ-lyon1.fr/software/seaview.html
Sequence Manipulation Suite
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.
URL: http://bioinformatics.org/sms2/
Vienna RNA Package
RNA Secondary Structure Prediction and Comparison.
URL: http://www.tbi.univie.ac.at/~ivo/RNA/
WinGene
A tool for the analysis of nucleotide sequences.
URL: http://www.ipw.agrl.ethz.ch/~lhennig/wingene.html
X3DNA
3DNA is a versatile package for analyzing and rebuilding three-dimensional nucleic acid structures, based on a standard reference frame.
URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/
FreeTree
Freeware program for construction and bootstrap (and jackknife) analysis of phylogenetic trees from binary data (RAPD, RFLP, AFLP etc.)
URL: http://www.natur.cuni.cz/~flegr/programs/freetree.htm
GeneTree
GeneTree is an experimental program for comparing gene and species trees.
URL: http://www.stats.ox.ac.uk/~griff/software.html
PHYLIP
PHYLIP is a free package of programs for inferring phylogenies.
URL: http://evolution.genetics.washington.edu/phylip.html
PhyloDraw
PhyloDraw is a drawing tool for creating phylogenetic trees. It supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams.
URL: http://pearl.cs.pusan.ac.kr/phylodraw/
TreeView
TreeView X is an open source program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs).
URL: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/index.html
Genome Workstation
Genome Related Links at Roslin Institute, UK
URL: http://www.ri.bbsrc.ac.uk/genome_workstation/workstation.html
Genomes OnLine Database (GOLD 1.0) : -
A monitor of complete and ongoing genome projects world-wide.
URL: http://wit.integratedgenomics.com/GOLD/
Glimmer
A system for finding genes in microbial DNA, especially the genomes of bacteria and archaea.Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
URL: http://www.tigr.org/software/glimmer/
Glimmer HMM
A fast and accurate gene finder based on a GHMM architecture,
developed specifically for eukaryotes. It incorporates splice site models adapted from the GeneSplicer program and uses interpolated Markov models for evaluating the coding regions.
URL: http://www.tigr.org/software/GlimmerHMM/
Glimmer M
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
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
URL: http://www.tigr.org/software/mummer/
PDRAW
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/
PrimerDesign
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
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
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/
Pajek
Program for Larger Network Analysis.
URL: http://vlado.fmf.uni-lj.si/pub/networks/pajek/default.htm
PIN
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
Taverna is a tool for creating and running bioinformatics workflows.
URL: http://taverna.sourceforge.net/
WinPep
A versatile tool for the analysis of amino acid sequences.
URL: http://www.ipw.agrl.ethz.ch/~lhennig/winpep.html
MOLMOL
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
A program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
URL: http://www.avatar.se/molscript/
Rasmol
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
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/raster3d/raster3d.html
SPDBViewer
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/
Cellware
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/
CytoScape
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
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
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/
KineMage
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/kinemage/magepage.php
LOOPP
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
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 desk. 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
NAMD
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
It is a free program for protein structure model-building, visualization, validation and analysis.
URL: http://noc.ibp.ac.cn/
OpenBable
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/
Reduce
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/software/reduce.php
TraX
TraX (Trajectory eXplorer) is a simple Biodesigner-like program working under 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/download.html
VEGA
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/
ALIGN:-
Optimal Global Alignment of Two Sequences with No Short-cuts
URL: http://www.biochem.ucl.ac.uk/bsm/dbbrowser/ALIGN/ALIGN.html
PROCHECK :-
Evaluates the quality of a protein structure by Roman Laskowski, University College, London
URL: http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
PROVE :-
Analysis of Protein Atomic Volumes at UCMB, Belgium
URL: http://www.ucmb.ulb.ac.be/UCMB/PROVE/
WHAT IF :-
A versatile structure analysis program for mutant prediction, structure verification, molecular graphics and more by Gert Vriend, EMBL, Germany
URL: http://swift.cmbi.ru.nl/servers/html/
Protein sequence analysis
http://www.nbif.org/education/tutorial.php#Tutorial1
http://ndbserver.rutgers.edu/structure-finder/tutorials/index.html
http://www.mcc.ac.uk/hpc/mantec/training/bioinformatics/tools/InetToolsBio_26.html
http://www.library.csi.cuny.edu/~davis/Biochem_3521/pronuclinfoweb.html#PROTEIN
Metabolic pathways
http://www-unix.mcs.anl.gov/compbio/PUMA/Production/puma.html
Function prediction
http://www.genome.ad.jp/manuscripts/GIW95/Oral/GIW95O05.html
http://www.cs.uga.edu/~eileen/bioinform/tsld023.htm
Structure prediction & analysis
http://www.bmm.icnet.uk/people/rob/CCP11BBS/flowchart2.html
http://ismb00.sdsc.edu/tutorials/samudrala.html
http://www.biochem.ucl.ac.uk/~shepherd/ss-intro.html#why_is
http://www.embl-heidelberg.de/predictprotein/predictprotein.html
http://www.bmerc-www.bu.edu/psa/