Activities  
  Programmes  
Facilities
Services
Gallery
    People

Home
About Us
Links
Contact Us
Site Map


Institute of Biochemistry, Molecular Biology and Biotechnology
90, Cumaratunga Munidasa Mawatha, Colombo 03
Sri Lanka
Telephone : +94 11 2552528
Fax : +94 11 2552529
 

Databases :        Expand All | Contact All

  • Primary sequence databases
    • EMBL (European Molecular Biology Laboratory nucleotide sequence database)
    • GenBank (at National Center for Biotechnology information, [NCBI])
    • DDBJ (DNA Data Bank Japan at CIB)
  • Protein sequence databases
    • SWISS-PROT (Swiss Institute of Bioinformatics [SIB])
    • TrEMBL (Translated EMBL:computer annotated protein sequence data [EBI])
    • PIR-PSD (PIR-International Protein Sequence Database)
    • UniProt (Joined data from Swiss-Prot, TrEMBL and PIR)
    • UniRef (UniProt NREF (Non-redundant REFerence) database at EBI)
    • IPI (International Protein Index; human, rat and mouse proteome database [EBI])
  • Carbohydrate databases
    • CarbBank (Former complex carbohydrate structure database, [CCSD])
  • 3D structure databases
    • PDB (Protein Data Bank cured [RCSB])
    • EBI-MSD (Macromolecular Structure Database [EBI])
    • NDB (Nucleic Acid structure Datatabase [Rutgers State University])

Database search :        Expand All | Contact All

  • Text-based
    • ENTREZ (Search for nucleotides, proteins, genomes, structures, populations sets and literature)
    • SRS (Search EMBL, SWISS-PROT, TrEMBL, PIR, PDB, etc.)
    • DBGET/LinkDB (Integrated database search of LinkDB)
    • SSS (Sequence and structure searching site)
    • Molecules R US (Full text search of the PDB database)
    • MIA (Molecular Information Agent searching biological databases to find the existing information about a macromolecule)
  • Sequence-based (sequence similarity search)
  • Motif-based
    • ScanProsite (Find protein sequences matching PROSITE or other patterns)
  • Structure-based (structure similarity search)
    • VAST (Structure-structure similarity search at NCBI, US)
    • DALI (Protein structure comparison with PDB at EBI,UK)
    • Finding 3D Similarity by CE(Combinatorial Extension) or CT(Compound Likeness)
    • LIBRA (Search sequences homologous to a given structure by Inverse Folding Protocol)
  • Mass-based protein search
    • ProteinProspector
    • PeptIdent
    • Prowl
    • Mascot
    • MassSearch

Analysis tools :        Expand All | Contact All

  • DNA sequence analysis tools
    • Restriction; Detect repeats and unusual patterns
      • Restrictionmapper
      • Webcutter (Restriction analysis)
      • RepeatMasker (Search interspersed repeats and low complexity sequences)
      • REPuter (Fast computation of maximal repeats in complete genomes)
      • dnadot (Find regions of similarity in two sequences & repeats within a single sequence)
      • Blast 2 Sequences (Compare two sequences < 150 kb to trace repeat sequences)
      • LALIGN (Finds multiple matching subsegments in two sequences)
    • Align sequences
      • Align (Pairwise sequence alignment with GAP,SIM, NAP, LAP2 or GAP2)
      • MAP (Multiple alignment of (long) sequences without penalizing large gaps)
      • ClustalW
      • Launcher: multiple alignment (Choose from different alignment applications
      • AMAS (Analyze multiple aligned sequences
      • CINEMA (Colour INteractive Editor for Multiple Alignments)
    • Find genes
      • Sixframe (Translate DNA sequence in all 6 possible frames)
      • ORF Finder (at NCBI)
      • GeneMark (Species-specific search for genes)
      • GeneScan (Species-specific search for genes cfr. WebGeneMark)
      • GeneWise (Compares a protein sequence to a genomic DNA sequence)
      • GeneMachine (Integrated comparative and predictive gene identification)
      • NetPlantGene (Prediction of splice sites in Arabidopsis)
      • AAT (Analysis and Annotation Tool for finding genes in genomic sequences)
    • Find transcriptional elements
    • Find tRNA
      • tRNAscan-SE (Search for tRNA genes in genomic sequence)
      • FAStRNA (Predict potential tRNA genes in genomic sequences)
    • Other tools
  • RNA analysis tools
  • Protein sequence and structure analysis tools
    • Physicochemical properties
      • ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)
      • ProTherm (Thermodynamic Database for Proteins and Mutants)
    • Analyse primary sequence
      • ProtScale (Hydrophobicity, other conformational parameters, etc.)
      • SAPS(Statistical Analysis for charge clusters,repeats,hydrophobic regions etc.)
      • SignalP (Prediction of peptide signal sequence )
      • TargetP (Prediction of subcellular localization )
      • PSort(Prediction of signal sequence,transmembrane regions & protein localization)
      • NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins)
      • NetPhos (Prediction of phosphorylation sites in eukaryotic proteins)
      • Scansite (Prediction of phosphorylation sites and protein binding sites)
      • Helical Wheel (Representation of alpha-helical peptides)
      • Other primary sequence analysis tools
    • Alignment
    • Predict secondary structure
      • TMpred (Prediction of membrane-spanning regions and their orientation at ISREC)
      • TMHMM (Prediction of transmembrane helices in proteins at CBS)
      • SOSUI (Prediction of Transmembrane Regions)
      • PSort (Prediction of signal sequence, transmembrane regions and protein localization)
      • DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method)
      • HMMTOP (Prediction of transmembrane helices and topology of proteins)
      • TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur)
      • PredictProtein (Protein secondary structure prediction)
      • JPred (Protein secondary structure prediction )
      • HNN (Hierarchical Neural Network secondary structure prediction)
      • PSIpred (Protein secondary structure prediction)
      • nnPredict (Protein secondary structure prediction)
      • Other secondary structure prediction tools
      • BTPRED (Prediction of beta-turns)
      • Coils (Prediction of coiled Coil regions Lupas' method)
      • PairCoil (Prediction of coiled Coil regions by Berger's method)
      • MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies)
      • TOPS (Protein topology cartoon generation)
    • Analyse and model 3D structure
      • 3D viewers
        • RasMol (Free offline 3D viewer)
        • Swiss-Pdb Viewer (Deep View)
        • Chime (Browser plugin for structure view)
        • Cn3D (Browser plugin for structure view used in ENTREZ/STRUCTURE)
        • WebMol (Online 3D viewer)
      • 3D analysis
        • TOPS (Protein topology cartoon generation)
        • DOMPLOT (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts)
        • OCA (Structure database browser)
        • STRUCTURE (Molecular Modeling Database MMDB)
        • PsiPred (Sequence profile based fold recognition)
        • Predicting Protein 3D structure based on homologous sequence search
        • 123 (Fold prediction by aligning (threading) to a (set of) structure(s) )
        • LOCK (Compare 3D structures of query and target proteins (PDB codes) and visualize superposed 3D structures )
        • CE (3-D protein structure comparison and alignment using the combinatorial extension (CE) method )
        • DALI (Automated Protein Structure Alignment)
        • LIBRA (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence )
        • VAST (Structure-structure similarity search)
        • ASC (Analytic Surface Calculation of PDB molecules)
        • PDB Retriever
        • MolSurfer (Calculate and navigate protein-protein interfaces)
        • Protein-Protein Interaction Server
      • 3D homology modeling
        • CPHmodels (Structure prediction by comparative homology modeling)
        • Swiss-Model (Automated protein homology-modeling server)
        • 3DCrunch (Browse database of modeled Swiss-Prot proteins)
        • FAMS (Fully Automated Modeling Service )
        • 3D-Jigsaw (Comparative modeling server at Imperial Cancer Research Fund)
        • SDSC1 (Protein structure homology modeling server)
        • Meta PP (Collection of structure prediction services)
  • Tools for protein function assignment
    • Scan or search for patterns, motifs, profiles, domains, families
      • ScanProsite (Scan a protein sequence against PROSITE pattern database)
      • PROSCAN (Scan a protein sequence against PROSITE pattern database allowing mismatches)
      • PPSearch (Scan a protein sequence against PROSITE pattern database with graphical output)
      • PFSCAN (Scan protein against different profile databases)
      • FingerPRINTScan (Scan a protein sequence against protein motif fingerprints database PRINTS)
      • BLOCKS Search (Scan a protein against BLOCKS database)
      • eMOTIF-Scan (Scan for motifs that describe protein families or superfamilies)
      • Scansite (Prediction of protein signaling sequence motifs)
      • MEME (Multiple EM for Motive Elicitation: Motive discovery)
      • eMotif-maker (Build motifs that describe protein families or superfamilies)
      • Meta-MEME (Buid motif at San Diego Supercomputer Centre)
      • CDART (Conserved Domain Architecture Retrieval Tool)
      • SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
      • InterProScan (Search a protein against the integrated protein domains and functional sites database InterPro)
      • CD-Search (Search a protein against conserved domain database CDD with RPS-BLAST)
      • COGnitor (Search a protein agains the COG database)
      • iProClass Search (Search a protein against PIR's integrated protein class database)
      • SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
      • PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)
      • ProDom (Automatically generated protein domain database at Toulouse)
      • Modules (Mobile protein domains database)
      • SBASE (Protein domain library)
      • HSSP (Database of homology-derived structures and sequences of proteins)
      • 3Motif (Find protein (domain)s with defined 3D motifs)
      • eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices)
      • GeneQuiz (Automated analysis of protein sequences)
    • Search, computation and analysis of pathways
      • KEGG (Search and computation tools at KEGG pathway database)
      • aMAZE (Query tools for metabolic and signal transduction pathway analysis)
    • Protein-protein interactions
      • DIP (Search Database of Interacting Proteins)
      • MINT (Molecular INTeraction database)
      • BioGRID (General Repository of Interaction Datasets)
      • STRING (database of predicted functional associations among genes/proteins)
      • InterPrets (Interaction prediction through structure)
    • Protein Annotation
      • AAT (Analysis and Annotation Tool for finding genes in genomic sequences)
      • Artemis (Free (large-) DNA sequence viewer and annotation tool)
      • Gene Ontology tools (Universal function annotation vocabulary)
    • Automatic alert for related new sequence
      • PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases)
      • Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)
      • New microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)
  • Phylogenetic Analysis
  • Microarray Data Browsing and Analysis
© Institute of Biochemistry, Molecular Biology and Biotechnology