My Dedication to the Bioinformatics Community

Love in speech is truth. Love in action is righteousness. Love in thought is peace. Love in understanding is non-violence.

--- Sathya Sai Baba---



Educational services

Java Scrap Book - your own techno- tutorial hub
Big Data Interview Questions
NCBI bioinformatics mini-courses
2canBioinformatics -bioinformatics educational
3-D Modeling of Proteins
37-523 Computational Biology 2002-03
3rd Regional Training Courses in Bioinformatics Ap
A database of 3D enzyme active site templates
A Glossary for Systems Biology
A List of Gene Finding programs
A mini HTML lesson for beginners
A Series of Structural Method Tutorials
A Short Java Course
Advanced Bioinformatics Workshop - Course Page
Advanced Topics Course on Computational Systems Bi
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Alphabetical Directory of Linux Commands
Amos' WWW links page
Animal Bioinformatics and Computational Genomics
Autoimmune Diseases Online
Available Databanks at the Institut Pasteur
BayGenomics Useful web resources
BE561 DNA & Protein Sequence Analysis
Beginner's Guide to Python
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CRISP Thesaurus
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Databases at the Weizmann Institute of Science
Databases of interest for small molecule docking
Dictionaries Microsoft Reader Home Downloads
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DNA from the Beginning
DNA Motif and Structure Tools
DNAstuff : } ~ what stuff life is made of
DOE Joint Genome Institute programs of the U.S. Depart
DOLOP - A Database of Bacterial Lipoproteins
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linux tutorials - linux tutorials
List of Methods Pages for Genomics
Locating Binding Sites in Protein Structures
Manual Protein Superimposition
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Model Organism Databases
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Principles of Protein Structure Using the Internet
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Sequence Analysis
sequence morif search
Sequencing Projects Blast Search Services @ SANGER
Small Molecule SIG
Software in Catagory GDRM
South African National Bioinformatics Institute
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stanford Index of /class/cs262/Spring2003/Slides
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The comprehensive Universal Protein Resource down
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the Stanford MicroArray Database, stores raw
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Various Structural Biology Tutorials Vigyaan is an electronic workbench
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XML for Molecular Biology as compiled by Paul Gord
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Analysis Tools

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 kb to trace repeat sequences)

  • 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 and Heuristic GeneMarkat 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 Baylor College of Medicine (USA):

  • NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)

Find Transcriptional elements
  • 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)

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

Protein Function Assignment

Search Pattern, motif, Profiles domains, families
  • 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 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 the PROCAT database of 3D enzyme active site templates)

  • Meta-MEME (motive buiding at San DiegoSupercomputer 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 againstBLOCKS database; also searches PRINTS)

  • DART (Domain Architecture Retrieval Tool at NCBI, USA)

  • InterProScan or InterPro Search (Search a protein against the integrated protein domainsand 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

Protein Annotation
  • PAA (Protein Annotator's Assistant at EBI, UK)

  • Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Center, UK)

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 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

  • 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 toolsat 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)

3D Analysis
  • 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
  • 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)

Organism classification

Microarray data analysis

Microarray data analysis