Tools & Softwares

DNA Sequence Analysis Tools

Restriction, Detect repeats & unsual Patterns
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> Zinfo (Detection of unusual sequences in large DNAs at Virtual Genome Center), USA)

Align Sequences
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)

Find Genes

Webtrans (Translation and codon usage of very large sequences at Virtual Genome Center) GeneMark (Species-specific search for genes with WebGeneMark , WebGeneMark.hmm andHeuristic 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)

Find Transcriptional elements
Identification of Prokaryotic Promoters (Promotor prediction in <100> IHF Site/Sigma 54 Promoter searches (at Pensylvania State University, USA)	SignalScan (Identification of transcriptional elements in <100> FirstEF (first-exon and promoter prediction program for human DNA at CSHL, USA)

Find t RNA
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)

Other Tools
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)

Protein Function Assignment

Search Pattern, motif, Profiles domains, families

ScanProsite (Search a protein sequence againstPROSITE pattern database at ExPASy, CH) PPSearch (Search a protein sequence againstPROSITE pattern database with graphical output at EBI, UK) FingerPRINTScan (Search a protein sequence against protein motif fingerprints databasePRINTS ) 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 CDDdomain 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 thePROCAT 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 againstPROSITE 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 againstBLOCKS 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 COGdatabase 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)

Search, computation & analysis of pathways
KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)	aMAZE (Query tools for pathway analysis at EBI, UK)

Protein-Protein interactions
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 )

Protein Annotation
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 )

Automatic alert for related new sequence
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 Analysis Tools
RNA Fold (Fold your own RNA sequences)	RNA World (Links to RNA resources from IMB Jena Biocomputing Group, Jena, Germ.)

Protein sequence & Structure

Physiochemcial Properties
ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)	ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)

Analyse Primary Sequence

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

Alignment

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)

Predict Secondary Structure

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)

Analyse & Model 3D Structure

3D Viewers
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 toSwiss-Model . Tutorial ) WebMol (Online 3D viewer at University of California, USA) WebMol (Online 3D viewer at EMBL)

3D Analysis

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)

3D Homology Modelling
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)

Phylogenetic Analysis

Mutiple sequence alignment
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

Organism classification
NCBI Taxonomy TreeBASE	The Tree of Life Project

Microarray data analysis

Microarray data analysis
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)