• DNA Sequence Analysis Tools
  - Restriction, detect repeats & unsual Patterns
  - Align Sequences
  - Find Genes
  - Find Transcriptional elements
  - Find t RNA
  - Other Tools
• Protein Function Assignment
  - Search Pattern, motif, Profiles domains, families
  - Search, computation & analysis of pathways
  - Protein-Protein interactions
  - Protein Annotation
  - Automatic alert for related new sequence

• RNA Analysis Tools
• Protein sequence & Structure Analysis Tools
  - Physiochemcial Properties
  - Analyse Primary Sequence
  - Alignment
  - Predict Secondary Structure
• Analyse & Model 3D Structure
  - 3D Viewers
  - 3D Analysis
  - 3D Homology Modelling
• Phylogenetic Analysis
  - Mutiple sequence alignment
  - Organism classification
• Microarray data analysis

• Webcutter (Restriction analysis)
• RepeatMasker (Search interspersed repeats and low complexity sequences)
• dnadot (Find regions of similarity in two sequences and repeats within a single sequence at Colorado State University, USA)
• LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)

• Tandem Repeats Finder (at Mount Sinai School of Medecine, NY, USA)
• Dot Plot (Compare a large sequence with itself at Virtual Genome Center)
• Blast 2 Sequences (Compare two sequences <150 kb to trace repeat sequences)
• Zinfo (Detection of unusual sequences in large DNAs at Virtual Genome Center), USA)

• Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
• ClustalW (at EBI, UK)
• Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
• CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)

• MAP (Multiple alignment of (long) sequences without penalizing large gaps)
• ClustalW (Multiple sequence alignment at WUSTL, USA)
• ClustalW (at the Baylor College of Medicine, USA)
• AMAS (Analyze multiple aligned sequences at Oxford University, UK)

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• Webtrans (Translation and codon usage of very large sequences at Virtual Genome Center)
• GeneMark (Species-specific search for genes with WebGeneMark , WebGeneMark.hmm and Heuristic GeneMark at Georgia Institute of Technology , USA)
• GenLang (Exon recognition at University of Pennsylvania, USA)
• GeneMachine (Integrated comparative and predictive gene identification at NHGRI, USA)
• AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)

• Sixframe (Translate DNA sequence in all 6 possible frames)
• ORF Finder (at NCBI)
• GeneMark (Species-specific search for genes cfr. WebGeneMark at EBI, UK)
• GRAIL (Exon recognition USA).
• Gene feature (Exon recognition, Promoter and Transcription Factor Binding Site Prediction, Open Reading Frame Identification.at Baylor College of Medicine (USA):
• NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)

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• Identification of Prokaryotic Promoters (Promotor prediction in <100 kb DNA at Lawrence Berkeley National Laboratory, USA)
• IHF Site/Sigma 54 Promoter searches (at Pensylvania State University, USA)

• SignalScan (Identification of transcriptional elements in <100 kb DNA sequences < 100 kb at BIMAS, University of Minesota, USA)
• FirstEF (first-exon and promoter prediction program for human DNA at CSHL, USA)

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• tRNAscan-SE (Search for tRNA genes in genomic sequence at Washington University, St Louis, US)

• FAStRNA (Predict potential tRNA genes in genomic sequences at Institut Pasteur, Paris, France)

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• CountCodon (Analyse codon usage in protein coding sequence at Kazuasa DNA Research Institute, Jp)
• DNA folding server (Fold secondary structures)
• Netprimer (Free online primer analysis at Premier Biosoft Int., Ca, USA)
• IMGT/V-QUEST an interactive tool for immunoglobulin and T cell receptor sequence analysis

• MAR-Finder (Search for matrix association regions at NCGR, Santa Fe, USA)
• Reverse Complement (Convert DNA sequence data to it's Reverse Complement.)
• PRIDE (Primer design atDFKZ, Heidelberg, Germany)
• PCR primer selection
  Primer3 (PCR primer selection tool at Whitehead Institute for Biomedical Research, US)
  GeneFisher (Interactive PCR primer design tool at the University of Bielefeld, Germany)

• ScanProsite (Search a protein sequence against PROSITE pattern database at ExPASy, CH)
• PPSearch (Search a protein sequence against PROSITE pattern database with graphical output at EBI, UK)
• FingerPRINTScan (Search a protein sequence against protein motif fingerprints database PRINTS )
• Scansite (Prediction of protein signaling sequence motifs at HIM, Boston, USA)
• SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
• CD-Search (Search a protein against CDD domain database, including Pfam and SMART, with RPS-BLAST at NCBI, USA)
• eMOTIF Search (Assign putative function to new proteins by sequence comparison with IDENTIFY motif database at Stanford University, USA)
• PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)
• Meta-MEME (motive buiding at San Diego Supercomputer Centre, SDSC, Ca, USA)
• eMOTIF Maker (Generate motifs that describe protein families or superfamilies ats Stanford University, USA)
• Modules (mobile protein domains database)
• HSSP (Database of homology-derived structures and sequences of proteins at EBI)
• eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)

• PROSCAN (Search a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)
• PFSCAN (Search protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)
• BLOCKS Search (Search a protein against BLOCKS database; also searches PRINTS)
• DART (Domain Architecture Retrieval Tool at NCBI, USA)
• InterProScan or InterPro Search (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)
• COGnitor (Search a protein agains the COG database at NCBI)
• iProCass Search (Search a protein against PIR's integrated protein class database at Georgetown University, USA)
• SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
• MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)
• ProDom (Protein domain database at Toulouse, Fr)
• DOMO (homologous protein domain families database)
• SBASE (Protein domain library at ICGEB, It)
• 3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Netscape and Chime plugin))
• GeneQuiz (Automated analysis of protein sequences at EMBL)

• KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)

• aMAZE (Query tools for pathway analysis at EBI, UK)

• DIP (Search Database of Interacting Proteins at UCLA, USA)
• PreBIND (Locate biomolecular interaction information in the scientific literature at the Samuel Lunenfeld Research Institute, Toronto, Canada )
• BINDBLAST (Search BIND database with BLAST)

• ProNet Online (Database of interacting proteins from Myriad Genetics, US)
• BIND (Biomolecular Interaction Network Database at the Samuel Lunenfeld Research Institute, Toronto, Canada )

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• PAA (Protein Annotator's Assistant at EBI, UK)
• Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Center, UK)

• AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
• AmiGO and other tools (Universal function annotation vocabulary by the Gene Ontology Consortium )

• Sequence Alerting System (E-mail alert for daily searched new homologues of query sequence at EMBL, Heidelberg)
• Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)

• PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
• Microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)

• RNA Fold (Fold your own RNA sequences)

• RNA World (Links to RNA resources from IMB Jena Biocomputing Group, Jena, Germ.)

• ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)

• ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)

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• ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
• ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
• SignalP (Prediction of peptide signal sequence at CBS, Denmark)
• TargetP (Prediction of subcellular localization at CBS, Denmark)
• NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
• NetPhos (Prediction of phosphorylation sites in eukaryotic proteins)
• Helical Wheel (Representation of alpha-helical peptides)
  

• Hydropathy plots (At Pensylvania State University, Department of Biochemistry and Molecular Biology)
• SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)
• PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
• DGPI (Prediction of GPI-anchor and cleavage sites, University of Geneva, CH)
• Scansite (Prediction of protein signaling sequence motifs at HIM, Boston, USA)
• Other primary sequence analysis tools at ExPaSy

• Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)
• ClustalW (Multiple sequence alignement at WUSTL, USA)
• Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
• AMAS (Analyze multiple aligned sequences at Oxford University, UK)
• CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)

• SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)
• ClustalW (at EBI, UK)
• ClustalW (at the Baylor College of Medicine, USA)
• MAP (Multiple alignment of (long) sequences without penalizing large gaps
• Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
• BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)

• TMpred (Prediction of membrane-spanning regions and their orientation at ISREC)
• SOSUI (Prediction of Transmembrane Regions, JP)
• DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
• TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)
• JPred (Protein secondary structure prediction at EBI)
• HNN (Hierarchical Neural Network secondary structure prediction at NPS@, Lyon, France)
• nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
• BTPRED (Prediction of beta-turns at UCL, UK)
• PairCoil (Prediction of coiled Coil regions, Bergers method)
• TOPS (Protein topology cartoon generation at EBI, UK)

• TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
• PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
• HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)
• PredictProtein (Protein secondary structure prediction at EMBL)
• Predator (Secondary structure prediction from single or multiple sequences at EMBL, Heidelberg)
• PSIpred (Protein secondary structure prediction at Brunel University, UK)
• Other secondary structure prediction tools at ExPASy
• Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
• MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI , USA)

• RasMol (Free offline 3D viewer. Download )
• Chime (Browser plugin for structure view from MDL Chemscape)
• Cn3D (Browser plugin for structure view used in ENTREZ/STRUCTURE from NCBI)

• Swiss-Pdb Viewer (Deep View) (Free offline 3D viewing and analysis application, tightly linked to Swiss-Model . Tutorial )
• WebMol (Online 3D viewer at University of California, USA)
• WebMol (Online 3D viewer at EMBL)

• TOPS (Protein topology cartoon generation at EBI, UK)
• 3DB Browser (Structure database browser at Weizmann Institute of Science, Israel)
• STRUCTURE (Molecular Modeling Database MMDB from ENTREZ at NCBI)
• Predicting Protein 3D structure based on homologous sequence search (EMBL Heidelberg, Germany)
• LOCK (Compare 3D structures of query and target proteins (PDB codes) and visualize superposed 3D structures at Stanford University, USA)
• VAST (Structure-structure similarity search at NCBI, US)
• ASC (Analytic Surface Calculation of PDB molecules at EMBL, Heidelberg)
• Protein-Protein Interaction Server (UCL, UK)

• DOMPLOT (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)
• GenTHREADER (Sequence profile based fold recognition on PSIpred server at Brunel University, UK)
• 123 (Fold prediction by aligning (threading) to a (set of) structure(s)
• DALI (Automated Protein Structure Alignment at EBI,UK)
• LIBRA (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading at NIG, Jp)
• MolSurfer (Calculate and navigate protein-protein interfaces at EMBL, Heidelberg)

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• CPHmodels (Structure prediction by comparative homology modeling at CBS, Denmark)
• 3DCrunch (Browse database of modeled Swiss-Prot proteins at ExPASy, Switzerland)
• SDSC1 (Protein structure homology modeling server at SDSC, USA)
• List of comparative modeling tools (at the Rockefeller University, NY, USA)

• Swiss-Model (Automated protein modeling server at ExPASy, Switzerland)
• FAMS (Fully Automated Modeling Service at Kitasato University, JP)
• 3D-Jigsaw (Comparative modeling server at Imperial Cancer Research Fund, London, UK )
• Meta PP (Collection of structure prediction services at Columbia University, USA)

• ClustalW (Multiple sequence alignement at WUSTL, USA)
• Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
• BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
• TaxPlot (3-way comparisons of genomes based on encoded proteins at NCBI)

• ClustalW (at EBI, UK)
• ClustalW (at the Baylor College of Medicine, USA).
• AMAS (Analyze multiple aligned sequences at Oxford University, UK).
• Entrez-PopSet (Search set of DNA sequences from populations of related individuals/organisms at NCBI)
• Phylogeny software

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• NCBI Taxonomy
• TreeBASE

• The Tree of Life Project

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• Expression Profiler ( Microarray data analysis at EBI , UK)
• ClustArray (DNA microarray data analysis
  at CBS, Denmark)

• TBI Expression Analysis (Find differential genes between two filter hybridisation experiments at DFKZ, Heidelberg)

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