Current efforts in molecular biology are producing an abundance of data that provides exciting opportunities for knowledge discovery, as well as an increasing problem of information overload. Bioinformatics concerns the development of new software and tools for the analysis of genomic and molecular biological data, which include

 

 

BIOCARTA is a web-based, user contributed collection of pathways and the tools to study them. Observe how genes interact in dynamic graphical models

Cell Illustrator is a biopathway modeling and simulation tool

Cognia Molecular is a tool for managing biological information.

GenMAPP (Gene Map Annotator and Pathway Profiler), is a computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes.

KEGG (The Kyoto Encyclopedia of Genes and Genomes) is a resource for metabolic pathways and regulatory pathways.

LION Target Engine(™) is a suite of programs for pathway and sequence analysis.

MetaCore is an integrated software suite for functional analysis of microarrays, SAGE, proteomics and other experimental data

Multifactor Dimensionality Reduction (MDR) is an open-source, freely available, and user-friendly software package for detecting and characterizing epistasis or gene-gene interactions in genetic and epidemiologic studies of common human diseases.

PathArt is a dynamic pathway articulator, which builds molecular interaction networks from curated databases

PathwayStudio (formerly PathwayAssist) is a powerful, user-friendly software package that allows you to build, visualize and explore biological association networks (BAN)

Pathways Analysis is a web-based application that makes use of Ingenuity Systems' Pathways Knowledge Base, a curated database of millions of modeled relationships between proteins, genes, complexes, cells, tissues, drugs and diseases.

The Pathway Tools software is a bioinformatics software system for pathway analysis of genomes, and for creating Pathway/Genome Databases (PGDBs)

Protein Networker enables an institute to make high throughput protein interaction data

Vector Xpression and Vector PathBlazer is a combined microarray and pathway analysis tool from Invitrogen. Vector PathBlazer software allows you to view protein-protein interactions

STRUCTURE PREDICTION

 

 

 

FGENEH from the Baylor College of Medicine predicts a single complete gene and the corresponding amino acid sequence.

GENSCAN, available from MIT, predicts complete gene structures in genomic sequences.

IDT's Biotools provides freely usable Internet access to software for oligonucleotide design for the PCR, secondary structure prediction, sequence similarity,

MSEQ is a user-friendly program which combines novel graphics and integration of predictive parameters from several sources for the prediction and display of protein secondary structures

MZEF, from CSHL, is a program that predicts internal protein coding exons in genomic DNA sequences.

NAB was designed to construct models of helical and non-helical nucleic acids from a few dozen to a few hundred nucleotides in size.

NAMOT(Nucleic Acid MOdeling Tool) is a tool developed at Los Alamos National Laboratory for the structural manipulation of single or double stranded, RNA or DNA. NAMOT uses a set of reduced co-ordinates to describe base/unit, sugar and phosphate geometry

Peptool is a software program which assists in the identification of protein function

PoPMuSiC, has been developed to predict protein stability changes upon single-site mutations

PROSPECT Pro is the latest release of the R&D 100 award-winning protein structure prediction tool

RAPTOR is an innovative software tool designed to predict protein structures from their sequence information.

SegMod provides the user with a completely automated method for homology modeling

SIGNALSCAN, a service from the NIH, finds homologies in published signal sequences based on the sequence submitted

SOPMA (Self Optimized Prediction Method from Alignment) is a package to make secondary structure predictions of proteins

3D-PSSM is a Browser-based protein fold recognition program which uses 1D and 3D sequence profiles coupled with secondary structure information (Foldfit)

WHAT IF is an extensive protein modeling, protein structure analysis, database handler, molecular graphics package

 

SEQUENCE ANALYSIS

 

AAT - Analysis and Annotation Tool from Michigan Tech University is used to identify genes by comparing cDNA and protein sequence databases.

ABI PRISM software products, from Applied Biosystems, provide advanced, automated analysis for the range of genetic analysis applications from fragment sizing to database matching to pedigree drawing.

AcaClone pDRAW32 is a freeware DNA cloning, analysis and visualisation software

AGCT Hybridization simulation and oligo analysis software especially suited for diagnostic, therapeutic, and common gene family research

AlleleID designs probes and primers for pathogen detection, bacterial identification, species identification and taxa discrimination using qPCR and microarray assays

Antheprot Protein analysis software

Array Designer 4: Design efficient, specific oligos for SNP genotyping and expression microarrays

arraySCOUTTM is a gene expression data analysis application

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features

Ancestor,designed to inferace ancestral amino acid sequence from set of homologous amino acid sequence whose phylogent relation is known

Asterias is a suite of freely- accessible web-based genomic data analysis programs

Beacon Designer 6: designs oligos for SYBR® Green, TaqMan®, LNA spiked TaqMan®, MethyLight, molecular beacon, NASBA® and FRET assays

Bio Image is a life sciences software information company which carries a wide variety of electrophoresis image analysis software for Windows, Powermac, and UNIX

BioinformatiX is an enterprise software which provides an environment for the analysis of microarray data

BioRainbow Analysis Tools are a collection of software tools for binding site prediction, weight matrix search, regulatory sequences analysis, microarray analysis, footprint

bioSCOUT® is a comprehensive and customizable bioinformatics package

BioTools offers three primary bioinformatics products: GeneTool for DNA sequence analysis, PepTool for protein sequence analysis, and ChromaTool for chromatogram analysis

BlockSearch is a quantitative method for the elucidation of unknown protein function

Clann: Software for investigating phylogenomic information using supertrees

CLC Free Workbench is a freeware bioinformatics software package

CURVES, by Richard Lavery and Heinz Sklenar is a very useful nucleic acid helical analysis program

DisTree it computes pairwise distance of allied nucleotide sequence utilizing various models of base substitution.

DNADynamois a general purpose software for DNA and Protein sequence analysis

DNASIS is a robust sequence analysis software package

DNPTrapper is a shotgun sequencing assembly editing tool, specifically designed for finishing and analysis of repeated regions

EuGene and SAm is a menus based DNA and protein sequence analysis package

Expression is a powerful application for DNA and protein sequence analysis

Genchek , developed by Ocimum Biosolutions is a comprehensive, LIMS based, user friendly Nucleotide and Polypeptide Sequence Analysis Tool

Genehound(™) offers a new, innovative, and exciting apporach to identifying coding regions in prokaryotic genomes

GeneInform is an easy-to-operate gene expression management and analysis tool

Gene Inspector(™)1.5: A powerful and versatile combination of an electronic laboratory notebook and sequence analysis package for biologists

GeneJockey is a program for editing, manipulation, and analysis of nucleic acid and protein sequences

GeneLinker products are the easiest way for researchers to start analyzing gene expression data

GENEMARK is a genefinding tool

GENEPARSER is a coding region recognition program

GeneSifter™, a Web-based microarray analysis system that combines data management and analytical functions with integrated, current gene annotation

GeneSolve is a single-User desktop sofware package for analyzing nucleic acid sequence infromation

GeneStudio Pro

GeneWorks - an integrated sequence analysis and database searching(http://www.genestudio.com/) is a newly developed suite of molecular biology programs

GenAL, programme for genomic alignment

Genemaster, used to manipulating gene sequence

Genie, from LBNL, is a gene finder based on generalized hidden Markov models to locate multi-exon genes

GENLANG is a syntactic pattern recognition system that uses tools of computational linguistics to locate genes.

GenomeBrowser is a powerful software tool that simplifies the proccess of analysis, annotation, and manipulation of genetic sequences

Genowiz, is a powerful gene expression analysis program designed to efficiently store, process and visualize gene expression data

GENSEARCH is a user-friendly locus specific software application assisting biologists in the analysis of DNA sequences

GLIMMER , is a program that uses interpolated Markov models to find genes in microbial DNA

GoCore V is a free, open source, "protein sequence alignment and analysis tool

Grail(™) Toolkit. best tools for identifying genes and proteins in the human genome

Genomix GrailEXP6 is created for recognizing splice sites, identifying exon/intron boundaries, and modeling genes.

Iditis - This package provided instant access to protein motifs, substructures and interactions buried in the Brookhaven databank

ISYS(TM), is the National Center for Genome Resources' new product that integrates independent bioinformatic software tools and databases

JalView, it used to view and edit alignment.

JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological pairwise local sequence alignment

LASERGENE is modular, for single users or networks, offering in-depth coverage of sequencing, primer design, sequence alignment, databases and database searching, protein analysis, and restriction map analysis

Look: is a set of informatics tools which allows the researcher to seamlessly access and manage protein sequences, structures

MEGA,a computational analysis of DNA and protein

Mummer, is a system for rapidly aligning entire genome

MacImdad was macromolecular modeling software

MacVector  is a set of sequence tools which conduct DNA sequence analysis

MORGAN, is a decision tree program for finding genes in vertebrate DNA.

MPSRCH: is a program which permits rapid searches of DNA and protein sequence data banks using the full Smith-Waterman algorithm

NeoBio is a Java class library of computational biology algorithms

NetPrimer: Performs and prints individual primer and pair analysis using the latest primer design software.

NEWHELIX is a software program for the analysis of oligonucleotide structure

OMIGA  sequence analysis tool

Onto-Express automates the process of annotating a set of expressed genes with genomic functions

PAP is a suite of programs to analyze protein structure

PatternHunter is a revolutionary general-purpose homology search tool based on well-recognized, innovative and proprietary technologies

PEAKS is software that identifies proteins and peptides using tandem MS data

PepSeq is a web based training software designed for online computer training of peptide sequencing techniques

Phylip,tool for drawing phylogenetic tree

Plasmid is a new Windows-based vector map drawing and sequence analysis program

PRIMER PREMIER 5: A fully featured, competitively priced primer design program to design specific, sensitive, high yield primers.

PROCHECK , is a program which conducts knowledge-based analysis of protein structures

PROCRUSTES, uses the spliced alignment algorithm, to examine all possible exon assemblies and finds the multi-exon structure with the best fit to related protein.

ProteinSolve is a single-User desktop sofware package for analyzing protein sequence infromation

Readseq, a tool for reading and editing nucleotide sequence

The Rosetta Resolver System, provides high-capacity data storage, retrieval and analysis of gene expression data.

RGBG Analyzer software is designed for color analysis of digital images

SEQtools 8.2 is a win32 software package for handling and analysis of nucleotide and protein sequences

Sms2, is a sequence manipulation suite for generating, formating and analysing short DNA and protein sequence.

Sectrace, designed to draw pictures ready for publication from secondary structure prediction

SIGNALSCAN, finds homologies in published signal sequences based on the sequence submitted

Solltech DNA fingerprinting and image analysis software

STEM (The Short Time-series Expression Miner) is a Java program for clustering, comparing, and visualizing short time series gene expression data

STRAP is an editor for the multiple sequence alignment of proteins

TESS (Transcription Element Search Software), is a system for locating and displaying transcription factor binding sites in DNA sequences.

TurboBLAST is an accelerated, parallel implementation of BLAST, a sequence comparison tool that provides critical insight into the structure and function of genes and proteins

UniPro DPview is a powerful tool for analyzing genetic sequences

Vector gives researchers the power to analyze proprietary sequences in the context of human genome project data.

VIBE (Visual Integrated Bioinformatics Environment). a next generation visualization and genomics discovery too

Visual Cloning 2000 is an advanced new vector map drawing and sequence analysis program

The Wisconsin Package for sequence analysis contains over 100 interrelated software programs. It enables scientists to analyze DNA and protein sequences by editing, mapping, comparing, and aligning them.

 

 

SEQUENCE MANAGMENT

BioMerge is a complete system for managing biological sequence data and related information

CLC Workbench is a freeware bioinformatics software package available for managing sequencing data

Gene Construction Kit(tm) 2: A DNA manipulation, cloning design, and illustration tool

GeneJockey is a program for editing, manipulation, and analysis of nucleic acid and protein sequences

GeneStudio Pro (http://www.genestudio.com/) is a newly developed suite of molecular biology programs

Starfruit system architecture specifically designed for clinical and forensic DNA testing

 

 

DOCKING SOFTWARES

HEX is a protein docking software used for molecular superimposition of various macromolecules

GRAMM a program for protein docking

GeneDoc is a tool for visulaizing , editing and analysing multiple alignment of genes.

3-D dock is a docking software for dock protein-protein as well as protein ligand.

GNU Dock is a tool for docking nucleiotide sequence.

Lig Builder used to construct ligand molecules with the constraints of target molecules.

Spack tool for docking macro-molecules

X-Score, gives graphical and stastitical score for docked product.

AutoDock is a docking software commonly used for docking all kind of protein and ligand.

 

 

MODELLING SOFTWARES

 

Cn3D allows to view 3D structures in graphyical view

Pymol is a molecule graphyical system with an embedded python interpreter designed for real time visualization

Rasmol is a graphyical interface to view molecules

Spdbv is to view and analyse macromolecules

Biodesigner is to design various molecules

Bodil used to protein structural and functional analysis and to ligand design

MDL Chime show 3D structues and run in browser as a plugin

MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure:

Shadybox, is package with set of library function targeted towards application developers who want a straightforward way to do simple 2D and 3D graph

Raster 3D is ued to generate high quality images of protein

MolMol is a graphyical interface programme

Viewerlite is a software used for view macromolecules in a 3D

WHAT IF is an extensive protein modeling, protein structure analysis, database handler, molecular graphics package

Visual Cloning 2000 is an advanced new vector map drawing and sequence analysis program

SimVector: Automates the production of publication quality graphics of vectors and provides sequence analysis to assist in the design of cloning experiments

Relibase is a web-based tool for searching and analysing protein ligand structures in the PDB

 

CHEM TOOLS

 

Chem2Pac used for computational chemistry

Cloning used for cloning of DNA

Cmap demo it show demo of maping o DNA in the sequence

DNA for window, it is special DNA toolused for sequence fumction and assembly

NAMD is a parallel object oriented dynamics code designed for high performance simulation of large biomolecules system

Plasmid plotter used to plot plasmid

VEGA is a computational chemistry tool

Surface reader used to measure the surface area calculation of macromolecules.

 

 

 

About Bioinformatics

Current efforts in molecular biology are producing an abundance of data that provides exciting opportunities for knowledge discovery, as well as an increasing problem of information overload. Bioinformatics concerns the development of new software and tools for the analysis of genomic and molecular biological data, which include

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