Tarun Gupta
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Bio-Computing Tools

It is a one-step platform for most of Bioinformatics activities. I have assembled most of the links on this page to make it easy for biocomputing users to access various resources online without wandering on google. Kindly report any broken links or if you have more resources to share. I shall incorporate them on this page. Happy Computing !

                          Index of links              

                                     

   

             DNA SEQUENCE ANALYSIS

 GENE PREDICTION

  1. EMBOSS at EBI
  2. Gene Finder at Sanger centre
  3. PredictGenes (Darwin) (Switzerland)
  4. SBDS sequence analysis
  5. Bipartite Nuclear Localisation Sequence Locator
  6. IUPAC-IUB Abbreviations and symbols for nucleic acids, polynucleotides and their constituents.
  7. GENSCAN at MIT (US) ***
  8. WebGeneMark
  9. GrailEXP at Oak Ridge (US)
  10. Genie at Berkeley (US)
  11. Gene Prediction Services

TRANSLATION

  1. EMBOSS at EBI
  2. ExPASy - Translate tool
  3. DNA Sequence Translation (ALCES)
  4. The Protein Machine (EBI)
  5. Nucleic Acid to Amino Acid Translation (London)
  6. Nucleic Acid to Amino Acid Translation (London - mirror)
  7. SeWeR is a DHTML interface for web based sequence analysis
  8. IUBMB Prokaryotic and eukaryotic translation factors.

ORF ANALYSIS

  1. EMBOSS at EBI
  2. ORF Finder (NCBI)
  3. ORF analysis (WebGene)
  4. FGENESH-2 Improving gene finding accuracy
  5. FGENESH HMM - Gene finding for mouse genes

TRANSCRIPTION FACTOR BINDING SITES

  1. TFSEARCH: Searching Transcription Factor Binding Sites
  2. MatInspector (Germany)
  3. Alibaba2 (Germany)

 

REPEATS

  1. EMBOSS at EBI
  2. Dot Plot Analysis THEORETICAL EXPLANATION
  3. Dot Plots (Colorado State University) (limit: 20.391bp x 20.391 bp)
  4. Dot Plot (to itself) (ALCES) (postscript/GIF output)
  5. Blast 2 Sequences (NCBI)

CODON USAGE

  1. Codon Usage Database
  2. Codon usage (ALCES)

CONTIG ASSEMBLY

  1. CAP sequence assembly at Infobiogen
  2. CAP Sequence Assembly at BCM Search Launcher

PATTERN SCAN

  1. PatScan

RESTRICTION ANALYSIS

  1. Webcutter 2.0 (USA)
  2. Webcutter 2.0 (USA)
  3. Webcutter 2.0 (Sweden)
  4. Restriction Enzyme Analysis (SUNY) (US)
  5. Restriction Maps (Colorado) (US)
  6. REMAP
  7. MBS - SeqCUTTER - On-line enzyme restriction analysis tool
  8. MULTI-CUT Restriction Endonuclease Buffer Data Base

 

OLIGO/PRIMER ANALYSIS

  1. WWW GeneFisher (Germany) ***
  2. PCR Aplification Assistant
  3. IDT OligoAnalyzer 2.0 (US) ***
  4. Oligonucleotide Calculator (USA) - simple
  5. GENSET OLIGOS - Oligo Calculation
  6. Tm Determination (ALCES) - simple
  7. pDRAW32 - freeware DNA cloning, sequence analysis and plasmid/DNA plotting software
  8. Oligonucleotide Calculator (USA) - simple
  9. WWW GeneFisher
  10. Primer3 at MIT (US)
  11. Primer3 (older version)
  12. Primer Selection (Text) (ALCES)
  13. NetPrimer (US)
  14. NCBI Blast short sequence
  15. Visual Cloning 2000 (Redasoft)
  16. PCR Box Titration Calculator v 0.93
  17. Alkami Biosystems: Primer Design Online
  18. Web Primer: DNA and Purpose Entry
  19. CODEHOP
  20. netprlaunch
  21. Tavi's PCR protocols

SEQUENCE ALIGNMENT

PAIRWISE SEQUENCE ALIGNMENT

  1. BCM: Pairwise Sequence Alignment
  2. Dot/matrix plots
  3. Dotmatrix program PPCMatrix
  4. LALIGN (france)
  5. Blast 2 Sequences (NCBI)
  6. SBDS: Pairwise Sequence Alignment (works only well for proteins)
  7. MBS - ALIGNER : CLUSTALW interface for multiple sequence alignement (did not work on netscape navigator)

MULTIPLE SEQUENCE ALIGNMENT

  1. BCM: Multiple Sequence Alignments
  2. IBC: Multiple sequence alignment (MSA)
  3. SAM: Sequence Alignment and Modeling System
  4. CLUSTALW at GenomeNet (Japan)
  5. ClustalW at EBI (UK)
  6. CLUSTALW at DDBJ (Japan)
  7. CLUSTALW at IBCP (WWW to EMAIL)
  8. GeneBee ClustalW 1.75
  9. CMBI CLUSTAL W
  10. MULTALIN at IBCP (WWW to EMAIL)
  11. MULTALIN + CLUSTAL at IBCP (WWW to EMAIL)

 

 

SEQUENCE HOMOLOGY SEARCHES

BLAST

  1. BLAST at NCBI (USA) - basic
  2. BLAST at NCBI (USA) - advanced
  3. BLAST against (un)finished Genomes at NCBI (USA)
  4. MEGABLAST at NCBI (large set of DNA query sequences)
  5. MEGABLAST at Harvard (large set of DNA query sequences)
  6. Search for short nearly exact matches of DNA sequences
  7. Search for short nearly exact matches of protein sequences
  8. PSI BLAST at NCBI (USA) - Position Specific Iterated BLAST
  9. BLAST 2 sequences
  10. BLAST at EBI (Hinxton, UK)
  11. BLASTall at EBI (Hinxton, UK)
  12. BLAST at GenomeNet (Japan)
  13. BLAST at BCM: DNA searches
  14. BLAST at BCM: Protein searches
  15. BLAST at PIR-International Protein Sequence Database
  16. BLAST search in PRODOM
  17. OWL BLAST Server
  18. GeneBee Basic BLAST 2.0
  19. Genebee Advanced BLAST 2.0

FASTA

  1. FASTA at EBI (Hinxton, UK)
  2. FASTA at NPS (France)
  3. FASTA Email server at EBI
  4. Fasta 3.3

SW (Smith-Waterman)

  1. Smith-Waterman (EBI)

BASED ON AA COMPOSITION

  1. AA composition: protein search (ExPASY)
  2. AA composition: PropSearch (EMBL)

DARWIN

  1. AllAll: Related peptide sequences
  2. AllAllDB: Querying the all-against-all database of SwissProt
  3. NuclPepSearch: Searching SwissProt for a nucleotide sequence
  4. PepPepSearch: Searching SwissProt for a peptide sequence

    AMINO ACID/PROTEIN INFORMATION

  1. Genetic Code Viewer
  2. single letter amino acid codes
  3. amino acid structures
  4. BRENDA the enzyme database
  5. IUBMB enzyme nomenclature
  6. IUPAC-IUB: phosphorus-containing compounds of biochemical importance
  7. IUPAC-IUB : synthetic polypeptides - Polymerised amino acids.

HYDROPHOBICITY PLOT

  1. Hydropathicity Plots at Colorado (US)

REVERSE TRANSLATION

  1. Reverse Translate a Protein at Colorado (US)

MOTIFS / PATTERNS SEARCHING

  1. NPS@ : PATTINPROT search
  2. PROSITE at EBI (Hinxton, UK))
  3. PROSITE at ExPASy (Switzerland)
  4. PRATT at EBI (input alignment) ***
  5. FPAT Regular Expression Searching Protein Databases
  6. MIPS ATLAS
  7. PatScan (also imperfect matches)
  8. ISREC PatternFind (WWW to EMAIL)
  9. Motif Explorer
  10. N-Glycosylation Site Prediction Server
  11. CBS prediction servers
  12. BNL motif searching
  13. SignalP signal peptide identification
  14. Sigfind signal peptide identification
  15. MOTIFS in SwissProt at IBCP (France)(WWW to EMAIL)
  16. PRINTS
  17. BLOCKS
  18. PRODOM
  19. SBASE
  20. MOTIF at GenomeNet (Japan)
  21. Protein Motifs (ALCES)
  22. PROTCOMP Identification of sub-cellular localization of eukaryoric proteins

 

PREDICTPROTEIN

  1. The PredictProtein server
  2. PPstatus: What is the PP backlog ?

 

STATISTICAL ANALYIS

  1. Statistical Analysis of Protein Sequences at EBI (Hinxton, UK)
  2. SAPS at ISREC (Switzerland)

DIGESTION PRODUCTS SEARCH

  1. MOWSE
  2. PROWL
  3. MassSearch: Searching SwissProt or EMBL by protein mass after digestion

PROTEIN SORTING / LOCALIZATION

  1. PSORT (Japan)
  2. PROTCOMP Identification of sub-cellular localization of eukaryoric proteins
  3. SignalP signal peptide identification

ISO-ELECTRIC POINT / MOLECULAR WEIGHT

  1. protein -> pI, MW and Composition
  2. protein -> pI and MW (EXPASY)

AMINO ACID COMPOSITION

  1. Protein -> AA composition (SBDS)
  2. Protein -> AA composition + analysis (SAPS at ISREC)
  3. AA composition -> protein search (EXPASY)
  4. AA composition -> protein search (EMBL)
  5. AA composition -> Sec. Str. (EMBL) (WWW to EMAIL)
  6. MBS - ProtCALC - protein parameters (pI, MW, aa composition, Extinction data)

 

SECONDARY/TERTIARY STRUCTURE PREDICTION

RNA

  1. RNA folding (Zuker)
  2. RNA folding (Zuker, older version, allows variable temp)
  3. RNA folding (Zuker; mirror at Wayne State University)
  4. RNA folding (Zuker; mirror in Australia)
    returns results by email only.

PROTEIN

  1. AGADIR An algorithm to predict the helical content of peptides
  2. SSCP Secondary structural content prediction from amino acid composition
  3. Southampton - SBDS - GOR
  4. CPHmodels - Homology modelling
  5. PREDATOR request form
  6. Southampton - SBDS - GOR
  7. IBCP secondary structure (France)
  8. Protein Explorer FrontDoor (Univ Mass)
  9. Protein Explorer FrontDoor (San Diego, faster)
  10. PredictProtein
  11. 3D-PSSM Protein Fold Recognition (Threading) Server (UK)
  12. Description of SSThread WWW service
  13. GENO3D : AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE
  14. BCM: Secondary Structure Prediction
  15. PREDATOR request form
  16. EMBL Dali: email server for 3-D protein structure database searches
  17. BCM PSSP
  18. CE Home Page - Combinatorial Extension
  19. SSCP: protein -> AA composition -> SS (EMBL) (WWW to EMAIL)
  20. SSCP: AA composition -> SS (EMBL) (WWW to EMAIL)
  21. TMAP (EMBL) (WWW to EMAIL)
  22. PDB to Animated Gif
  23. Download RASMOL
  24. Sander's 3-D Modelling homepage
  25. List of free molecular visualization programs
  26. Structural Biology Software Database
  27. MDL Information Systems, Inc | Chime Plug-in

PHYLOGENY

Software Programmes

  1. Joe Felsenstein's Phylogeny programs website
  2. Phylogenetic Analysis Computer Programs
  3. Phylogeny software (Glasgow University)
  4. TreeTop - Phylogenetic Tree prediction
  5. CMBI CLUSTAL W
  6. Puzzle: Tree reconstruction for sequences by quartet puzzling and maximum likelihood (Strimmer, von Haeseler)
  7. MacClade Home Page
  8. PAUP
  9. Morkov Chain Monte Carlo - phylogeteic analysis (USA)
  10. Morkov Chain Monte Carlo - phylogeteic analysis (UK)
  11. Morkov Chain Monte Carlo - Molecular clock
  12. TREECON download page (demo version)
  13. Phylogeny server at Pasteur
  14. SOAP Stability of aligned positions
  15. TreeEdit
  16. FORCON download page (sequence format interconversion for the PC only)
  17. Mesquite

Databases

  1. TreeBase at Harvard
  2. Aligned DNA and Protein sequences at EBI
  3. Molecular Evolution & Organelle Genomics

Info and tutorials

  1. Harvard Dept of MCB - More Biology Links
  2. Tree of Life Homepage
  3. Phylogenetic Analysis of Proteins (Fred Opperdoes)
  4. Introduction to Phylogeny

MEDLINE

  1. NCBI PubMed
  2. BioMedNet MEDLINE
  3. MEDLINE Alert service (at EMBL)
  4. BioMail, References from Medline to your e-mail account
  5. Biomail via Russia

3D PROTEIN IMAGES

Protein Database Brookhaven PDB/RSCB Protein Data Bank

  1. 3DB Browser (Brookhaven, main site)
  2. 3DB Browser (EBI, mirror)
  3. 3DB Browser (UK, mirror)
  4. 3DB Browser (Germany, mirror)
  5. 3DB Browser (Poland, mirror)
  6. 3DB Browser (France, mirror)
  7. PDB WWW Home Page
  8. PDB At A Glance
  9. PDB Retriever at DDBJ
  10. RCSB Protein Data Bank at SDSC (main)
  11. RCSB Protein Data Bank at Rutgers (mirror)
  12. RCSB Protein Data Bank at NIST (mirror)
  13. RCSB Protein Data Bank (all mirror sites)

CHIME 3D

  1. Chemscape Chime: download page
  2. Molecular Tutorials using Chemscape Chime from MDL Information Systems
  3. HIV-1 protease -- structure with indinavir

  

METABOLIC PATHWAYS

  1. BioCarta - Charting Pathways
  2. BRENDA the enzyme database
  3. SwissProt/TrEMBL
  4. Enzyme database
  5. Boehringer metabolic pathways
  6. KEGG metabolic encyclopedia
  7. KEGG metabolic encyclopedia2
  8. EMP - Enzymes and Metabolic Pathways Project
  9. aMAZE Protein function and biochemical pathways database
  10. Pedant
  11. WIT database
  12. COG (Clusters of orthologous Groups) database
  13. EcoCyc E.coli database
  14. Malaria parasite metabolic pathways
  15. List of metabolic pathway databases

 

CMS-SDSC MOLECULAR BIOLOGY RESOURCE

  1. The CMS-SDSC Molecular Biology Resource - France
  2. The CMS-SDSC Molecular Biology Resource - San Diego (US)
  3. The CMS-SDSC Molecular Biology Resource - Italy

                       

                         DNA/PROTEIN DATABASES

GENERAL DATABASE INFO

1.        Database Statistics (courtesy of DDBJ)

2.        Human Genome Sequencing

3.        GENBANK (NCBI)

4.        GENBANK SITEMAP

5.        EMBL (EBI)

6.        PDB Protein 3D database

7.        Nucleotide sequences at EBI

8.        Nucleotide sequences at GenBank

9.        MAGPIE - Multipurpose Automated Genome Project Investigation Environment

10.     DDBJ (DNA Data Bank of Japan)

11.     MBGD Microbial Genome Database

12.     HOX Pro DataBase (in Russia)

13.     HOX Pro DataBase (Mirror in the US)

14.     Expasy Home of SwissProt Protein database

15.     SWISS-PROT (ExPasy)

16.     The Sanger Centre

17.     Genome Monitoring Table (daily update EBI)

18.     MAGPIE

19.     NIH News Release 06/26/2000

20.     Enzyme Nomenclature

21.     TIGR Microbial Database

22.     Pfam Protein domain database at Sanger Centre

23.     The TIGR Trypanosoma brucei Database

24.     Trypanosome GeneDB at Sanger

25.     BMERC Completed Genomes collected resources

26.     DNA Sequence Collaborator's Page

27.     Genome Sequence Database GSDB (NCGR)

28.     PEDANT complete genome analysis

29.     C. elegans Database

30.     The Protein Research Foundation

31.     Population studies with PopSet with aligned DNA seqiences

32.     Extinct organisms in GenBank

33.     DBGET Database Document: GenBank

DNA Sequence Retrieval

1.        ENTREZ-Nucleotide query (NCBI)

2.        SRS at EMBL-EBI, Hinxton (UK)

3.        DNA Search (GenomeNet, Japan)

4.        GENBANK at NCBI

5.        Direct retrieval from EMBL via accession code

PROTEIN Sequence Retrieval

1.        ENTREZ-Protein query (NCBI)

2.        SRS at EMBL-EBI, Hinxton (UK)

3.        Protein Search (GenomeNet, Japan)

4.        SWISS-PROT and TrEMBL (Switzerland)

5.        RCSB Protein Data Bank (US)

6.        RCSB PDB Mirror Sites

7.        PIR-Web - The Protein Identification Resource (NONACTIVE)

8.        GENBANK using ENTREZ

9.        Protein Search (GenomeNet, Japan)

10.     Direct retrieval from EMBL via accession code

 

Vector screening

 

1.        VecScreen (NCBI)

2.        Vector Scanning (EBI)

3.        Vector Screening System (DDBJ)

 

HUMAN GENOME PROJECT

 

   NIH/NCBI HUMAN GENOME RESOURCES

 

1.        The Human Genome

2.        Entrez Genome view: MAPVIEWER

3.        LocusLink Introduction

4.        Human Genome Sequencing

5.        National Human Genome Research Institute (NHGRI)

6.        dbSNP Home Page

7.        NCBI Contig Build and Annotation Process

 

HUGO-Human Genome Organisation

 

1.        HUGO homepage

2.        HUGO human chromosomes page

3.        HUGO Gene Nomenclature Committee (HGNC)

 

GENECARDS

 

1.        GeneCards (Weizmann Institute, Israel)

2.        GeneCards mirror (Finland)

3.        GeneCards mirror (Germany)

4.        GeneCards mirror (Canada)

5.        GeneCards mirror (Japan)

 

 

     DDBJ/CIB HUMAN GENOMICS STUDIO

 

1.          DDBJ/CIB Human Genomics Studio

 

HGSC Human Genome Sequencing Center (Baylor College of Medicine)

  Welcome to Baylor HGSC

 

ONL Oak Ridge National Laboratory

 

1.        Human Genome Landmarks Poster

2.        Human Genome Project Information

 

          ETHICAL, LEGAL, SOCIAL ASPECTS

 

1.        Clinical and patient aspects (HUGO)

2.        Ethical, Legal and Social Implications (ELSI; NHGRI at NIH)

 

 

OTHER GENOME PROJECTS

 

EUKARYOTIC GENOME PROJECTS

 

1.        Mouse Genome Resources Page

2.        Rat Genome Resources Page

3.        Zebrafish Genome Resources Page

4.        Drosophila melanogaster @ NCBI

5.        Malaria Genetics & Genomics

6.        C. elegans project

7.        Arabidopsis thaliana

 

 

PARASITE GENOME PROJECTS

 

1.        Trypanosoma brucei Genome Project

2.        Leishmania Genome Network

3.        Trypanosoma brucei home page (at Sanger)

4.        Trypanosoma brucei Genome Network home page

5.        Trypanosoma brucei GSS sequences for downloading

6.        The TIGR Trypanosoma brucei Database

7.        Trypanosome GeneDB at Sanger

8.        Trypanosoma cruzi Blast search at TIGR

9.        Leishmania major home page (at Sanger)

10.     Leishmania Genome Network home page

11.     Leishmania major chromosome 15

12.     Leishmania major chromosome 26

13.     Leishmania major chromosme 28

14.     Leishmania Genome Network, Seattle, USA

15.     Parasite-genome database at EBI

16.     Parasite genome Blast server at EBI

17.     Parasite genomes databasesWHO Leishmania Genome Network Web site

18.     Malaria (Plasmodium falciparum genome map)

19.     Plasmo DB (Plasmodium Genome database)

 

MICROBIAL GENOME PROJECTS

 

1.        PEDANT complete genomes

2.        Entrez: microbial genomes taxonomy tree

3.        TIGR Microbial Database

4.        DDBJ Genome Information Broker

 

VIRAL GENOME PROJECTS

 

1.        Complete viral genomes (NCBI)

2.        Retroviruses

  

COMPARATIVE GENOMICS

 

1.   PEDANT CrossGenome categories

2.   COG: Clusters of Orthologous Groups of proteins( NCBI)

3.   TaxPlot (NCBI)

4.   HOBACGEN Homologous Bacterial Genes Database

5.   WIT Home Page

6.   KEGG Kyoto Encyclopedia of Genes and Genomes

7.   ERGO (Integrated Genomics, Inc.)

8.   LION bioscience | Products and Services | genomeSCOUTú

    

COMPLETE GENOMES AND GENOME PROJECTS

 

1.  GOLD Genome On line Database

2.  Proteome analysis at EBI

3.  All Available Complete Genomes

4.  GeneQuiz (Genome annotations)

5.  LocusLink (Human, Mouse and Rat Loci)

6.  Entrez Genomes Views (Human Chromosomes)

7.  Mitochon

 

We have some Bioinformatics suits to share. If any one could help me with background processing of executables, we would be able to showcase the softwares made by my classmates on this website. Any advice would be highly appreciated!