Bioinformatics Web Sites

This list contains pointers to various information sources in computational molecular biology. This is not an exhaustive listing and it only reflects what we found useful here at PBIL. Please report "dead" links to perriere@biomserv.univ-lyon1.fr.

General biocomputing services

• ReNaBi (France)
• GenomeNet WWW Server (Kyoto, Japan)
• Center for Information Biology (Mishima, Japan)
• Pôle Bio-Informatique Lyonnais (Lyon, France)
• European Bioinformatics Institute (Hinxton, UK)
• DKFZ Theoretical Bioinformatics (Heidelberg, Germany)
• ExPASy Molecular Biology Server (Geneva, Switzerland)
• National Center for Genome Resources (Santa Fe, USA)
• National Center for Biotechnology Information (Bethesda, USA)
• Swiss Institute for Experimental Cancer Research (Lausanne, Switzerland)
• Mobyle Portal at Pasteur Institute (Paris, France)

Molecular databases

General nucleotide databases

• EMBL (Hinxton, UK)
• Genbank (Bethesda, USA)
• DDBJ (Mishima, Japan)

General protein databases

• SWISS-PROT (Geneva, Switzerland)
• PROSITE (Geneva, Switzerland)
• PRODOM (Lyon, France)
• PIR (Washington DC, USA)
• PDB (San Diego, USA)

Specialized databases

• Prokaryotes
  • GenoList (Paris, France)
  • HGT-DB (Tarragona, Spain)
  • Genome division at NCBI (Bethesda, USA)
  • Genome Information Broker (Mishima, Japan)

• Eukaryotes
  • GDB (Baltimore, USA)
  • MGI (Bar Harbor, USA)
  • IMGT (Montpellier, France)
  • OMIM (Bethesda, USA)
  • Ensembl (Hinxton, UK)

• Complete genomes projects
• Genomes OnLine Database (Chicago, USA)
• Gene expression
• Sage GENIE (Bethesda, USA)

Retrieval systems

• DBGET (Kyoto, Japan)
• WWW-Query (Lyon, France)
• Public SRS servers (Cambridge, UK)

Alignments and similarity searches on-line

Similarity searches

• BLAST at NCBI (Bethesda, USA)
• BLAST at PBIL (Lyon, France)
• BLAST at ISREC (Lausanne, Switzerland)
• WU-BLAST at EMBL (Hinxton, UK)
• FASTA and SSEARCH at EBI (Hinxton, UK)

Pairwise alignments

• LFASTA at PBIL (Lyon, France) Local alignments
• SIM4 at PBIL (Lyon, France) Aligns cDNA and genomic DNA
• WISE2 at Pasteur (Paris, France) Aligns protein and genomic DNA
• SIM at ExPASy (Geneva, Switzerland)
• BLAST two sequences at NCBI (Bethesda, USA)
• SIM, GAP, NAP and LAP at Michigan Tech. Univ. (Houghton, USA)
• JAligner (Alexandria, Egypt) Java implementation of the Smith-Waterman algorithm

Multiple alignments

• BLAST+ClustalW at EMBL (Heidelberg, Germany) Multiple alignment of homologous sequences detected by BLAST
• ClustalW2 at EBI (Hinxton, UK) Display and edit alignments with JalView
• ClustalW at DDBJ (Mishima, Japan)
• ClustalW at GenomeNet (Kyoto, Japan)
• ClustalW at Pasteur (Paris, France)
• ClustalW at PBIL (Lyon, France) Colored alignments and secondary structure predictions
• Multalin at PBIL (Lyon, France) Colored alignments and secondary structure predictions
• Multalin at INRA (Toulouse, France) Colored alignments
• MAFFT at MiB (Fukuoka, Japan)
• MUSCLE at EBI (Hinxton, UK).
• DIALIGN2 at Pasteur (Paris, France)
• DIALIGN2 at BiBiServ (Bielefeld, Germany)
• DCA at BiBiServ (Bielefeld, Germany)
• MAP at Michigan Tech. Univ. (Houghton, USA)
• T-COFFEE at SIB (Lausanne, Switzerland)
• MATCH-BOX at MBR (Namur, Belgium)
• MAVID/AMAP at UCB (Berkeley, USA)
• BlastAlign at BioAfrica (Pretoria, South Africa)
Aligns nucleotide sequences that have large indels
• Kalign at the Karolinska Institute (Stockholm, Sweden)

Motif/Pattern/Profile searches

• PIMA II at BMERC (Boston, USA)

Methods

Gene recognition

• GeneMark at GeorgiaTech (Atlanta, UK)
• GrailEXP at ORNL (Oak Ridge, USA)
• GenScan at MIT (Boston, USA)
• GenScan at Pasteur (Paris, France)

DNA analysis

• Repeat Masker (Seattle, USA)
• Bend.it at ICGEB (Trieste, Italy)
• Signal scan service (Bethesda, USA)
• Promoter scan service (Bethesda, USA)
• Dragon promoter finder (Singapore)
• Elements of transcription (Neuherberg, Germany)

RNA analysis

• ESSA RNA software (Toulouse, France)
• The RNA world at IMB (Jena, Germany)

Protein analysis

• SignalP server (Lyngby, Denmark)
• ExPASy protein analysis tools (Geneva, Switzerland)

Downloadable software

• CodonW (Oxford, UK)

Bibliography

Documents

• Gene recognition bibliography (New York, USA)
• Biocomputing Course Resource List (Bielefeld, Germany)

Journals

• Gene
• Nature
• Science
• Bioinformatics
• Nature Genetics
• The BioInformer
• Nucleic Acids Research
• Journal of Biological Chemistry
• Molecular Biology and Evolution

Index of services in molecular biology

• The BioCatalog (Hinxton, UK)
• Institut Pasteur (Paris, France)
• Bioinformatics links (Lyngby, Denmark)
• Atelier de BioInformatique (Marseille, France)
• Bioinformatics software on the Web (Baltimore, USA)
• Amos Bairoch's WWW links page (Geneva, Switzerland)