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Main categories with sub-categories for Software

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• Databases
• Organizations
• Publications
• Software
• 2DE
• Bioinformatics
• Languages
• Mass spectrometry
• Microarrays
• Online tools
• Other
• Protein
• Sequence analysis
• Systems Biology
• Subject information
• Techniques

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• Delta2D (Decodon)
• Dymension (Syngene)
• Gellab II+ (Scanalytics)
• HT Analyzer and HT Analyzer Evolution Software (Genomic Solutions)
• ImageMaster (GE Healthcare)
• PDQuest (Bio-Rad)
• ProFINDER (PerkinElmer)
• Progenesis (Nonlinear Dynamics)
• Z3 and Z4000 (Compugen)

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• DeCypher Interface
• GeneSpring Analysis Platform (Agilent)
• Helical Wheel Java Applet
• iMolTalk - Structural Bioinformatics Toolkit
• MedMiner -text filters for gene, gene-gene or gene-drug queries
• Multiple Sequence alignment Version 2.0
• Protecs (Decodon)
• RasMol Home Page
• SEQUEROME - sequence profiling tool (BCBU, Georgetown University)
• The Open Bioinformatics Foundation
• Visible Human Server
• VMD - Visual Molecular Dynamics
• YASARA - Yet Another Scientific Artificial Reality Application -molecular graphics tool

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• BioJava
• MySQL - Open Source Database
• PHP - Hypertext Preprocessor
• Proteomics Standards Initiative - Molecular Interaction XML Format Documentation Version 1.0
• The Bioperl Project - Perl tools for bioinformatics, genomics and life science research
• XHTML 1.0 The Extensible HyperText Markup Language (Second Edition)

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• ExPASy - Aldente Peptide Mass Fingerprinting tool
• MSight - A new vision in Mass Spectrometry Imaging
• Phenyx - protein and peptide identification (GeneBio)
• Phenyx - the next generation of MS protein characterization software from GeneBio developed in collaboration with SIB
• Protein Prospector -for mining sequence databases in conjunction with MS
• SearchXLinks
• SEQUEST - Jimmy Eng & John Yates

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• GeneSifter - (VizX Labs)

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• BioTech resource (University of Texas at Austin,)
• IBM Bioinformatics and Pattern Discovery Group / MUSCA: Multiple Sequence Alignment
• Proteomic Tools -(ISB)
• Research tools - online tools (Protocol online)
• Research tools - software (Protocol online)
• SMART - Simple Modular Architecture Research Tool
• WebLogo - a sequence logo generator

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• Adobe Reader - Download
• EBI Tools: Blast, Fasta, Sequence Analysis, Homology Searches, Sequence Translation, Protein Annotat
• ExPASy - Tools
• ExPASy life sciences directory
• Oracle Technology Network
• SWEET - for contructing 3D models of saccharides (German Cancer Research Center, Heidelberg)
• The Apache HTTP Server Project

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• 2ZIP - Server -Leucine Zipper prediction
• 3D-JIGSAW Protein Comparative Modelling Server
• Biotech Validation Suite for Protein Structures
• BLAST search (protein-protein) at NCBI
• Calculate Molecular Weight and Isoelectric Point
• ChloroP 1.1 Prediction Server -predicts chloroplast transit peptides (cTP) in protein sequences
• CINEMA -Colour INteractive Editor for Multiple Alignments
• DAS Transmembrane Prediction server
• DisEMBL 1.4 - Predictors of intrinsic protein disorder
• ELM - Functional Sites in Proteins
• ExPASy - ProtScale
• ExPASy proteomics tools
• GENO3D - automatic modelling of protein 3D structure
• GlobPlot 2.1 - Predictor of intrinsic protein disorder/globularity/domains
• HelixDraw v1.00 - Helical Wheel Drawing Applet
• HNN secondary structure prediction
• Jpred - A consensus secondary structure prediction server
• KohGPI: Identification of GPI-anchor signals by a Kohonen Self Organizing Map
• LipoP 1.0 Server -Prediction of lipoproteins and signal peptides in Gram negative bacteria
• Mascot (Matrix Science)
• Mitoprot -Prediction of mitochondrial targeting sequences
• Multicoil Scoring Form
• P-val FingerPRINTScan
• PATS - identifies amino acid sequences that are potentially targeted to the apicoplast matrix of Plasmodium falciparum
• PepMapper
• Peptide mass calculator (Ron Beavis)
• PlasMit - Webinterface for Prediction of Localization of Plasmodium falciparum proteins
• Predicting Secreted Proteins of Mycobacterium Tuberculosis with a Bioinformatic Approach
• PredictProtein: structure prediction and sequence analysis
• PRINTS -a compendium of protein fingerprints.
• PROCHECK - protein structure checks
• PROF - Secondary Structure Prediction System
• Profound - search engine matching peptide masses to protein sequences (Genomic Solutions)
• ProteinInfo - protein sequence search engine for matching motifs (Genomic Solutions)
• Relibase - for searching protein-ligand databases.
• SAWTED - Structure Assignment With Text Description
• Scanps 2.3 -Scan Protein Sequence - for comparing a protein sequence to a database of protein sequences (EBI)
• Sonar ms/ms - search engine to identify proteins using peptide digest MS/MS data -(Genomic Solutions)
• SUMOplot - explain larger MWs than expected on SDS gels
• SWISS-MODEL -An Automated Comparative Protein Modelling Server
• SYFPEITHI: Epitope prediction
• The PSIPRED protein structure prediction server
• THREADER Info Page -protein structure prediction
• TLS Motion Determination (TLSMD)
• WHAT IF -a versatile molecular modelling for proteins and other molecules in their environment
• YinOYang 1.2 Server -neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences

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• 2ZIP - Server -Leucine Zipper prediction
• AMAS Server -Analyse Multiply Aligned Sequences
• Blocks WWW Server -(Fred Hutchinson Cancer Research Center)
• ClustalW
• ClustalW server -(EMBnet.org)
• COILS - Prediction of Coiled Coil Regions in Proteins
• CPHmodels-2.0 Server -homology modeling
• DIALIGN - multiple alignment
• EBI ANALYSIS TOOL
• FUGUE -Sequence-structure homology recognition
• Genolist server
• Graphical Codon Usage Analyser
• HHpred - Homology detection & structure prediction by HMM-HMM comparison
• Hydrophobic cluster analysis
• IBM Bioinformatics and Pattern Discovery Group / MUSCA: Multiple Sequence Alignment
• Isotopident - theoretical isotopic distribution
• MPsrch - a biological sequence sequence comparison tool (Smith and Waterman algorithm)
• NCBI-BLAST2
• PPSearch - search for protein motifs (EBI)
• Pratt - search for patterns conserved in sets of unaligned protein sequences (EBI)
• Protein Prospector -for mining sequence databases in conjunction with MS data - (UCSF)
• PSA Analysis Request -(BMERC)
• PSORT - family of programs for subcellular localization prediction
• Radar -Rapid Automatic Detection and Alignment of Repeats in protein sequences (EBI)
• REP - search a protein for repeats (EMBL)
• SAPS - Statistical Analysis of Protein Sequences (EBI)
• Scanps 2.3 -Scan Protein Sequence - for comparing a protein sequence to a database of protein sequences (EBI)
• Simmonics - alignment and analysis of nucleic acid sequences
• STRAP - Multiple Sequence Alignment (Humboldt University Berlin)
• TMAP multiple sequence alignment formTMAP
• TMHMM Server, v. 2.0 -Prediction of transmembrane helices in proteins
• TMpred - Prediction of Transmembrane Regions and Orientation
• Tools for alignment
• TopPred -Topology prediction of membrane proteins (Heijne, Wallin, Claros, Deveaud, Schuerer )
• WebLogo - Create Sequence Logos
• Wise2 - compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors (EBI)
• WU-Blast2 blast

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• Modas (Nonlinear Dynamics)
• Systems Biology Workbench

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