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Molecular Biological Link

Part I:

1. Important Home Pages
2. Manuals
3. Other Guides & Tutorials
4. Molecular Genetic Information
5. Genomic Sequence Databases
6. Other Genomic Databases and Utilities
7. Sequence Search & Retrieval
   1. Integrated Database Retrieval Systems
8. Sequence Identification (BLAST, FASTA etc.)
9. Sequence Alignment
10. cDNA Databases
11. Mutation Databases
12. New Sequence Submission
13. Open Reading Frame (ORF) Finder
14. Sequence Translation
15. Protein Sequence Databases
16. Motif Databases
17. Protein 3D Structure Database
18. Protein Analysis Utilities
19. PCR Primers and Probes
20. Databases of Non-Human Sequences
21. Utilities for Non-Human Sequences

Important Home Pages

[Top]

• European Molecular Biology Laboratory (EMBL)
  http://www.ebi.ac.uk/ebi_docs/embl_db/ebi/topembl.html
  Cambridge, UK.
• UK Human Genome Mapping Project - Resource Center (HGMP-RC)
  http://www.hgmp.mrc.ac.uk/
• SeqNet: UK Node of European Molecular Biology Network (EMBNet)
  http://www.seqnet.dl.ac.uk/
• GenBank
  http://www.ncbi.nlm.nih.gov/Web/Search/index.html
  GenBank at the National Center for Biotechnology (NCBI) of The National Library of Medicine (NLM) at The National Institutes for Health (NIH) campus, USA.
• DNA Databank of Japan (DDBJ)
  http://www.ddbj.nig.ac.jp
  
• Genome Sequence DataBase (GSDB)
  http://seqsim.ncgr.org/
  The National Center for Genome Resources, Genome Sequence Database.
  The server is a supercomputer with genomic algorithm accelleration.
• Online Mendelian Inheritance in Man (OMIM)
  http://www3.ncbi.nlm.nih.gov/Omim/searchomim.html
  Database of human genes and their disorders, with textual information, images and references. Links to Entrez and MedLine.
• European Drosophila Genome Project
  http://edgp.ebi.ac.uk/
• The Institute for Genomic Research (TIGR)
  http://www.tigr.org/
• The Sanger Centre
  http://www.sanger.ac.uk/
• Swiss Institute of Bioinformatics (Expasy)
  http://www.expasy.ch/
• GenomeNet (Japan)
  http://www.genome.ad.jp/
• Australian National Genomic Information Service (ANGIS)
  http://morgan.angis.su.oz.au
• Bioinformatics and Biology Resources on the Internet
  http://aeiveos.wa.com/biology/index.html
  An excellent site, well worth a visit!
• List of other Genome Sites
  http://www.hgmp.mrc.ac.uk/GenomeWeb/
  List of other genome web sites. Concise and clearly presented.
• Brunel University Online Teaching Programme
  http://www.brunel.ac.uk/depts/bl/project/front.htm

Manuals

[Top]

• EMBL
  http://www.ebi.ac.uk/ebi_docs/embl_db/usrman/usrman.html
• GenBank
  ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt
• SRS
  http://www.sanger.ac.uk/srs/srsman.html

Other Guides and Tutorials

[Top]

• BioComputing Hypertext Coursebook
  http://www.techfak.uni-bielefeld.de/bcd/Curric/
  A very thorough source of learning. Especially good for readers who want to get to grips with the "nuts and bolts" of bioinformatics.

Molecular Genetic Information

[Top]

• Gene Cards (*)
  http://bioinfo.weizmann.ac.il/cards/
  A very useful site providing comprehensive information and links. Direct links to GenBank, SWISS-PROT and MedLine. Includes synonyms, similar genes in other organisms, gene products and details about disorders.
• Gene Cards: Diseases with a Genetic Association (*)
  http://bioinfo.weizmann.ac.il/cards-bin/listdiseasecards http://bioinfo.weizmann.ac.il/cards/cards-bin/listdiseasecards
  View the complete (comprehensive!) list, or search for disease related genes by chromosome.
• Life Science Dictionary
  http://biotech.chem.indiana.edu/pages/dictionary.html
  A dictionary.

Genomic Sequence Databases

[Top]
These are the four primary sequence databases. They exchange sequence information daily.

• European Molecular Biology Laboratory (EMBL)
  http://www.ebi.ac.uk/ebi_docs/embl_db/ebi/topembl.html
  Cambridge, UK.
• GenBank
  http://www.ncbi.nlm.nih.gov/Web/Search/index.html
  GenBank at the National Center for Biotechnology (NCBI) of The National Library of Medicine (NLM) at The National Institutes for Health (NIH) campus, USA.
• DNA Databank of Japan (DDBJ)
  http://www.ddbj.nig.ac.jp
  
• Genome Sequence DataBase (GSDB)
  http://seqsim.ncgr.org/
  The National Center for Genome Resources, Genome Sequence Database.
  The server is a supercomputer with genomic algorithm accelleration.

Other Genomic Databases and Utilities

[Top]
These are often specialised databases.

• The International Immunogenetics Database (IMGT)
  http://imgt.cnusc.fr:8104
  Contains expertly annotated sequences and alignment tables for Ig, TCR and MHC sequences.
• Human Genome Map Database (HuGeMap)
  http://www.infobiogen.fr/services/Hugemap
  Genetic and physical maps of the human genome. Connected with the gene radiation hybrid mapping database RHdb.
• UTR Home Page
  http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRHome/
  Internet resources for sequence analysis of 5' and 3' untranslated regions of eukaryotic mRNAs. Includes specialised UTR databases and tools for analyses of UTR regions.

Sequence Search & Retrieval

[Top]

• Integrated Database Retrieval Systems

  • Entrez
    http://www.ncbi.nlm.nih.gov/Entrez/
    Start here for pretty much anything!
  • Sequence Retrieval System (SRS)
    http://www.seqnet.dl.ac.uk/srs/srsc
• The Institute for Genomic Research (TIGR), Human Gene Index (HGI) Sequence Search
  4-1-2-DDPDE/USA
  http://www.tigr.org/tdb/hgi/searching/hgi_seq_search.html
  Search for nucleotides and peptides.
• TIGR HGI Reports
  3-1-2-DDcW/USA
  http://www.tigr.org/tdb/hgi/hgi_info.html
  Retrieve sequences identified by EST ID, GenBank number etc.
• TIGR HGI Gene Expression Data
  4-2-1-DDcW/USA
  http://www.tigr.org/tdb/hgi/searching/hgi_xpress_search.html
  Search for tissue specific transcripts e.g. "lung". cDNA libraries can also be searched.
• TIGR HGI Name Search
  5-1-2-DDW/USA
  http://www.tigr.org/tdb/hgi/searching/hgi_name_search.html
  Search for a sequence by the name of a gene product e.g. insulin.
• Genome Database (GDB)
  http://hgmp.mrc.ac.uk/gdb or http://gdbwww.gdb.org/
  Funding for this project has been withdrawn. This valuable database will remain online, but it should be noted that no new entries will be recorded after 31st July 1998.
• GENATLAS (*)
  5-5-2-DUWI/France
  http://bisance.citi2.fr/GENATLAS/
  A comprehensive, easy to use site. Search gene, marker or phenotype or linkage databases. Useful, relevant links provided in the results. The user can also locate the desired gene from a graphical clickable map of disease related or other mapped genes on a chromosome.
• Gene Cards (*)
  http://bioinfo.weizmann.ac.il/cards/
  A very useful site providing comprehensive information and links. Direct links to GenBank, SWISS-PROT and MedLine. Includes synonyms, similar genes in other organisms, gene products and details about disorders.

Sequence Identification (BLAST, FASTA etc.)

[Top]

• The Sanger Centre Database Search Services
  5-2-5-DDPDFWE/UK -Clean, simple design.
  http://www.sanger.ac.uk/DataSearch/
  BLAST and WU-BLAST 2.0 searches which can be refined to finished and/or unfinished genomic sequences.
• BLAST 2 Similarity Search (EMBNet)
  5-3-2-PUWE/Switzerland
  http://www.ch.embnet.org/software/frameBLAST.html
  WU-BLAST 2.0 similarity searches.
• BLAST2 Search with Post-processing (EMBL)
  4-3-2-PUW/Germany
  http://dove.embl-heidelberg.de/Blast2/
  WU-BLAST 2.0 search with post-processing.
• FASTA 3 (EMBL)
  http://www2.ebi.ac.uk/fasta3/
  FASTA 3 similarity search.
• FASTA
  http://www2.igh.cnrs.fr/bin/fasta-guess.cgi
  FASTA similarity search and a clean, basic and simple interface.
• Blitz
  http://www.ebi.ac.uk/searches/blitz.html
  
• Beauty
  http://dot.imgen.bcm.tmc.edu:9331/seq-search/protein-search.html
  Beauty is an enhanced BLAST search, returning output which predicts the function of the protein being tested.

Sequence Alignment

[Top]

• Analysis and Annotation Tool for Finding Genes in Genomic Sequences
  5-3-2-DcDPDFWE/USA
  http://genome.cs.mtu.edu/aat.html
  Identifies genes in a DNA sequence by comparing it to cDNA and protein sequence databases (including those at HGI, TIGR, dbEST, Swiss-Prot and nr).
• Pairwise Sequence Alignment
  3-4-2-DcUPUFWE/USA
  http://genome.cs.mtu.edu/align/align.html
  Computes the global alignment between two sequences. Compare DNA with DNA, cDNA or protein. For DNA and cDNA, settings (gap open penalty, gap extension etc.) can be defined.
• Multiple Sequence Alignemnt with MAP
  4-3-2-DcUPUFWE/USA
  http://genome.cs.mtu.edu/map/map.html
  Calculates the global alignment of DNA or protein sequences using an algorithm which computes the best overlapping alignment without penalising terminal gaps. Long internal gaps in short sequences are not penalised.
• Network Protein Sequence Analysis
  5-4-1-PUW/France
  http://pbil.ibcp.fr/NPSA/npsa_clustalw.html
  ClustalW multiple sequence alignment.
• ALIGN
  5-1-1-DUPUWE/France
  http://www2.igh.cnrs.fr/bin/align-guess.cgi or http://genome.eerie.fr/fasta/align-query.html
  Applies the BLOSUM50 matrix to deduce the optimal alignment between two sequences.
• Multiple Sequence Alignment with Hierarchial Clustering
  5-5-3-PUW/France
  http://www.toulouse.inra.fr/multalin.html
  Sequence alignment with a colour output where differing or similar amino acids in the alignment can be highlighted.
• Colour INteractive Editor for Multiple Alignments (CINEMA)
  http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2.1/
  A comprehensive and popular site. Allows the user to visualise and manipulate aligned protein sequences.
  Makes use of Java. I recommend you access this site from a fast workstation!
• VSNS BioComputing Division Multiple Alignment Resource Page
  http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/
  An excellent, comprehensive resource for multiple sequence alignment, software and tutorials.

cDNA Databases

[Top]

• TIGR Human cDNA Mapping Project
  5-1-1-DcW/USA
  http://www.tigr.org/tdb/hummap/hummap.html
  Search by STS to retrieve individual STS reports, by GenBank, THC or HC number for transcripts with mapped STS's or by Chromosome number to see a list of all of the transcripts mapped to date, for example, on chromosome 16.
• Via OMIM
  You can search for a 'disease gene' at OMIM. Click the "DNA" button in the results display and follow the link to the mRNA sequence. Note the absence of U (uracil): this sequence is referred to in GenBank reports as mRNA, but the sequence is a cDNA sequence.
  http://www.nih.gov

Mutation Databases

[Top]

• Human Gene Mutation Database
  4-2-2-DUW/UK
  http://www.uwcm.ac.uk/search/mg/allgenes?
  Enter a GDB accension number, disease name, gene name or symbol to retrieve well presented information about the different mutation types, information and links.
• Protein Mutation Database
  Check this site!
  http://www.genome.ad.jp/htbin/bfind_pmd
  COMMENTS
• MITOMAP
  Check this site!
  http://infinity.gen.emory.edu/mitomap.html
  Mitochondrial DNA database.
• Breast Cancer Mutation Database
  Check this site!
  http://www.nchgr.nih.gov/Intramural-research/lab_transfer/bic/
  COMMENTS

New Sequence Submission

[Top]

• EMBL
  http://www.ebi.ac.uk/subs/emblsubs.html
• BankIt (GenBank)
  http://ncbi.nlm.nih.gov/

Open Reading Frame (ORF) Finder

[Top]

• ORF Finder
  http://www.ncbi.nlm.nih.gov/gorf/gorf.html
  Finds likely open reading frames in a sequence.

Sequence Translation

[Top]

• Nucleotide to Protein (Expasy)
  5-2-1-DUW/Switzerland
  http://www.expasy.ch/www/dna.html
  Translates a nucleotide sequence (DNA/RNA) into a protein sequence (amino acids).
• Nucleotide to Protein (EMBL)
  5-4-1-DUW/UK
  http://www.ebi.ac.uk/contrib/tommaso/translate.html
  Translates a nucleotide sequence into a protein sequence.
• Forward and Reverse Translation
  5-5-2-DUPUFWE/UK
  http://www.sanger.ac.uk/Software/Wise2/genewiseform.shtml
  Translate a protein sequence into a genomic DNA sequence, and vice versa.
  This is a WWW interface to the pgwise software application. Those who are proficient with this package may like to take advantage of it's extra capabilities by adding execution critera.
• Protein and cDNA Translation
  5-4-2-DcUPU/UK
  http://www.sanger.ac.uk/Software/Wise2/protein2cdna.shtml
  Translate a protein sequence into a cDNA sequence, and vice versa.

Protein Sequence Databases

[Top]

• Translated EMBL (TrEMBL)
  http://www.ebi.ac.uk/pub/databases/trembl
  Database of all the protein coding regions stored in the EMBL database. Comprehensive, but (generally) at the cost of poor annotation.
• SWISS-PROT
  http://expasy.hcuge.ch/sprot/sprot-top.html
  A database of protein sequences, translated from the EMBL genomic database. Protein sequences have been checked and annotated.
• PIR
  http://www_nbrf.georgetown.edu/pir/
  Four databases: PIR1 is the most comprehensive with entries classified and annotated. PIR4 is the least comprehensive, with unencoded or untranslated entries.

Motif Databases

[Top]

• Pratt Search (EMBL)
  4-4-2-PU
  http://www2.ebi.ac.uk/pratt/
  Interactively identifies conserved patterns from a series of user-entered unaligned protein sequences.
• PROSITE (via EBI)
  http://www2.ebi.ac.uk/ppsearch/
  Pattern search to identify conserved functional amino acid motifs. Scans a sequence against PROSITE (the primary motif database) with a graphical output.
• PROSITE
  http://expasy.hcuge.ch/sprot/prosite.html
  The primary motif database. Take care! Motifs are often short, and a large number of false positives should be expected! Options are available to exclude those which most commonly lead to false results.
• Protein Motif Fingerprints
  http://www.biochem.ucl.ac.uk/bsm/dbbrowser/PRINTS.html

Protein 3D Structure Database

[Top]

• Protein Databank
  http://www2.ebi.ac.uk/pdb/index.shtml
  Three dimensional protein structures which can be downloaded and viewed locally (viewer required) or viewed in a hypertext browser window (e.g. Netscape). The structures are experimentally determined by X-ray crystallography and nuclear magnetic resonance (NMR) imaging.

Protein Analysis Utilities

[Top]

• Web Cutter - Restriction Enzyme Mapping Utility
  http://www.medkem.gu.se/cutter/
  Map restriction enzyme sites on your sequence. Easy to use and comprehensive options.
• Protein Colourer
  5-2-1-PUW/UK
  http://www.ebi.ac.uk/htbin/visprot.pl
  Colour a protein sequence (raw text or SWISS-PROT Acc. No.) by properties e.g. hydrophobicity.
• Residue Periodicity
  Review this site
  http://o2.dbuoa.gr/FT/
  Study the periodicity of residues in a protein sequence.
• Compute the Theoretical pI and M_r
  5-1-2-PUW/Switzerland
  http://www.expasy.ch/ch2d/pi_tool.html
  Calculates the theoretical pI or molecular mass of a protein, whose sequence is entered by the user, or referred to as a SWISS-PROT or TrEMBL entry.
• Random Protein Sequence Generator
  5-5-2-PUW/Switzerland
  http://www.expasy.ch/sprot/randseq.html
  Random protein sequence generator! Output in FASTA format (the format most commonly required by bioinformatics search sites).

PCR Primers & Probes

[Top]

• Primer 3
  5-5-2-DUW/Norway
  http://www2.no.embnet.uio.org/primer/primer3.cgi?
  Select PCR primers for your nucleotide sequence.
• HGMP-RC Primers Database
  http://www.hgmp.mrc.ac.uk/local-data/Primers.html
• EBI Primers Database
  http://www.ebi.ac.uk/primers_home.html
• Molecular Probe Data Base (MPDB or MOLPROBE)
  http://www.biotech.ist.unige.it/interlab/mpdb.html

Databases of Non-Human Sequences

[Top]

• Berkeley Fly Database
  5-5-2-DDW (UI)/USA
  http://www.fruitfly.org/bfd/
  Search for sequences by name or map location, and optionally view a clickable image of sequenced contigs aligned alongside the fly chromosomes. Searches can be limited to available sequences only. Retrieve P1, BAC or cosmid genomic clones, P element insertion lines, YAC, STS and more.
• The Institute of Genomic Research Databases
  http://www.tigr.org/tdb/tdb.html
  Many databases including microbial, parasites, human, human cDNA, mouse, rat, Arabidopsis, zebrafish, and others.

Utilities for Non-Human Sequences

[Top]

• European Drosophila Genome Project BLAST server
  5-4-3-DDPDFWE/UK
  http://edgp.ebi.ac.uk/www-blast.html
  Search using the WU-BLAST 2.0 (gapped aligned) or the original BLAST (which does not allow gaps). The database includes Drosophila genomic data, EST's, STS's, P element sites, transposons, repeats, and proteins.
• Berkeley Drosophila Genome Project BLAST Searches
  5-4-3-DDFWE/USA
  http://www.fruitfly.org/blast/
  Search for your sequence using the WU-BLAST 2.0 algorithm for D. melanogaster sequence data, including EST's, genomic sequences, STS's or sequences derived from them, P element insertion sites and transposons.

  ---

  ---

  Part II:

  • AC3D Modeller and its manual
  • Alscript 2.0 and some examples
  • ARP Refinement Program
  • Babel
  • CCP4; its FAQ; its manual (also in PDF format) and its Newsletter; Scala v.2.7.1 (Jan. 2000)
  • CHIME (web page interactive manipulation of macromolecules)
  • Crystallography & NMR Software (CNS)
    • CNS_solve 0.9 (Yale University site)
    • CNS_solve (local)
    • Obtaining CNS
    • Tutorial
  • DENZO and SCALEPACK from HKL Research
  • DPS-MOSFLM (Data Processing Suite from Purdue Univ.)
  • ESPOIR (reverse Monte Carlo with powder diffr. data)
  • FINDNCS - NCS finding from heavy atom sites
  • Gimp
  • GLRF reference manual
  • GRASP or this additional site
  • ImageMagick
  • INSIGHT (which includes DELPHI)
  • MAR-Research & software
  • Molscript
  • MOSFLM and its user manual
  • O:
    • Main resources:
       |  T.A.Jones  |  M.Kjeldgaard  |  G.Kleywegt  | 
    • Background colour and more by Mark Harris in Uppsula
    • Ball-interface for O
    • Essential commands
    • Extract a sphere of atoms (script)
    • FAQ
    • Figures etc..
    • Manual
    • Mouse Function Keys (O 6.2)
    • Newsgroup archive
    • OPLOT 1.15 ftp site
    • Resources by M. Kjeldgaard
    • Space groups symmetry operators (230 space groups)
  • Povscript (from Dan Peisach) and manual POVRAY and its manual
  • Rasmol
  • Raster3D
  • Rayscript
  • Rayshade
  • Replace which includes GLRF, TF and ANGCAL (from L. Tong)
  • Setor
  • Shake and Bake and its anonymous ftp site nexus.hwi.buffalo.edu
  • SHARP / BUSTER
  • SHELX 97-2
  • SOLVE
  • Strategy (manual)
  • Structure factor tutorial
  • TNT
  • Uppsula Software Factory:
    • | DEJAVU | RAVE | VOIDOO | X-UTIL |
      | MOLEMAN | MAPMAN | OOPS | SPASM or SPASM-ftp |
    • Dept Molecular Biology (Uppsala)
    • Documentation for available softwares
    • Environment variables used for RAVE and other programs
    • HIC-UP Hetero-compound Information Centre
    • Tutorials
  • VMD
  • X-PLOR
    • A.T.Brunger's Lab
    • Department Store
    • manual (ver. 3.1)
    • Resources
    • Topology and Parameter library
  • XRayView
  • XtalView
  • XV

  - - - IUCr list of Software - - -
  

  Crystallography

  • Crystallization and Cryocrystallography:
    
    • BMCD: Biological Macromolecule Crystallization Database
    • Generating your Crystallization Experiments
    • Gitay's Practical guide to cryo-crystallography
    • Mineral and gemstone
    • Reannealing of frozen crystals
    • XACT - Working with crystallization conditions
  • Crystallographic Spreadsheets (EXCEL, PC format)
  • European Macromolecular Crystallographer List
  • Figures of molecules and/or electron density:
    • Examples of various formats with scripts
    • Introduction on making images using O with examples
    • Povscript (from Dan Peisach)
    • Stereo images using Molscript or Ribbons
  • Interactive Structure Factor Tutorial
  • International Union of Crystallography, and its Annual Meeting
  • LLNL Macromolecular Crystallography Web Site
  • Multiple Anomalous Dispersion (MAD):
    • MAD theory and literature
    • Scaling of MAD data by Philip R. Evans
  • Obituaries:

    • Sir David C. Phillips (now Lord Phillips of Ellesmere).

      See Nature 399, 26 (1999); also in formats .pdf and postscript

  • Protein Stereochemistry Analysis:
    • Atlas of side-chain and main-chain hydrogen bonding
    • DDQ (van den Akker & Hol (1999) Acta D55: 206-218)
    • Macromolecular structure validation
    • Papers: Good model-building and refinement practice
    • PARVATI from E.A.Merritt
    • Secondary structure sketch, using TOPS (by Janet Thornton)
    • Protein Structure Validation Server
    • Tabulated Ramachandran plot outliers
    • Whatcheck analysis
  • Representative set of high resolution crystal structures
  • Summer Course in crystallography
  • Twinning:
    • Bacteriorhodopsin case study (excellent!)
    • Data Reduction from Twinned RNA Crystals (ACA abstract)
    • Discussion by D. Watkin
    • Online discussion about twinning
    • SHELX97 also deals with twinning
    • Todd Yeates server

  DATABASES

  • BMCD: Biological Macromolecule Crystallization Database or use this other site
  • Cambridge Structure Database (CCDC)
  • DALI (protein structure comparison)
  • Database of Interacting Proteins (DIP)
  • Drug Structure Databank
  • EC Enzyme Database
  • Heavy-Atom Databank
  • Intein database server (at NEB)
  • ModBase - Database of comparative protein structure models
  • Molecular Structures Database (free until Sep. 1, 1999)
  • Nucleic Acid Database
  • PROMISE (Prostetic groups and metal ions in protein active sites)

  • Protein DataBank (PDB): <search>
    • 
      
    • Detailed transition plans to Rutgers University
    • Documentation and Information
    • ftp to PDB (archives)
    • How to link to a specific PDB entry
    • Molecules R US (at the NIH)
    • Obsolete PDB entries (Useful!!)
    • Processing status of entries 'ON HOLD'
    • Search Lite
    • Submit data to PDB (AutoDep Input Tool)

  • RELIBase (ligand search in PDB)
  •  

  Biology / Genetics

   |  Biology Benchwork  |  BLAST  |  Entrez  | 
   |  ExPasy & SwissProt  |  IMAGE  |  N.C.B.I.  |  PubMed  | 
   |  Material Safety Data Sheets  |  Genomes-Entrez  | 

  • BiologyWeek newsletter
    from the Whitehead Institute for Molecular Research
  • Biosciences at Harvard
  • Brutlag (Bioinformatics)
  • Centrifuges: rotor calculation
      (rpm and × g calculation for a great variety of rotors)
  • CNN Science & Technology
  • Dana-Farber Cancer Institute Molecular Biology Core Facility
  • Electron micrographs of organisms (the Nanoworld Image Gallery)
  • EMBL-Heidelberg
  • Eukaryotic organelle genomes (e.g. mitochondria)
  • GCG manual
  • Molecular Virology at the University of Wisconsin
  • Owl database search
  • Pedro's BioMolecular Reasearch
  • Roaches and cockroaches
  • Signal Transduction Knowledge Environment (part of Science online)
  • Visual embryos

  BACTERIA

  • American Type Culture Collection
  • E. coli Genetic Stock Center
  • E. coli Genome Center
  • E. coli Index (a lot about this bacteria)
  • E. coli Open Reading Frames (very large tables)
  • Microbial Underground
  • Salmonella Genetic Stock Center
  • Sites with extensive links
  • Veterinary bacteriology - Dictionary (French)
  • Who's who amongst bacteria: (up-to-date)
    
    • Bacterial species nomenclature
    • List of bacterial names with standing in nomenclature

  BIOCHEMISTRY

  • E. coli metabolism
  • Enzyme Datasheets:

    • Wortington Catalog's

      SWISS-PORT search

  • Metabolic Pathways (Washington University, DC)
  • Pathways: glycogen & glucose (animated glycolysis)
  • Protein-Diseases Database
  • Protein Kinase Resource

  GENOMICS

  • Camilla Kao web page with genomics links
  • Comparative genomics:
    • Bacillus subtilis  genome server
    • Campylobacter jejuni
    • Corynebacterium diphtheriae  NCTC 13129
    • Helicobacter pylori  26695
    • Helicobacter pylori  J99
    • Mycobacterium tuberculosis  H37Rv
    • Pseudomonas Genome Project
    • Pyrococcus furiosus  and this additional site
  • DNA microarray:
    • Albert Einstein College of Medicine
    • ArrayExpress Database
    • ATGC Consortium
    • Cornell Univ. site (by Andreas Matern)
    • European Bioinformatic Institute
    • George Church lab (Harvard Med. School)
    • GRID IT (Viginia Tech / NC State)
    • M-Guide: Pat Brown's manual to build and use a microarrayer
    • Microarray Centre - Ontario Cancer Institute
    • National Cancer Institute
    • National Genome Research Institute
    • Pat Brown's lab (which includes the microarrayer)
    • Puces-ADN (Server at the CNRS, France)
    • Research Genetics
    • Seigel-C Protocols
    • Silicon Genetics
    • Stanford DNA Microarray Database
  • DNA microarray: Data analysis:
    • Autoscan 1.0
    • Clustering Analysis (by M. Eisen, Stanford Univ.)
    • ExpressDB Information Page (John Aach and Wayne Rindone, Harvard Univ.)
    • Microarray & Data Analysis (Wentian Li, Rockefeller Univ.)
    • Microarray Analysis (Supplement to Aug. 6, 99 issue of Science)
    • Stanford MicroArray Database
  • GeneCensus Genome Comparison
  • Gene-Chips.com (DNA Microarrays)
  • Microbial genomics discussion group
  • Sanger Sequencing Center
  • Deborah Schegg's Homepage
  • TIGR Microbial Genome Database (completed and in progress)

  MOLECULAR BIOLOGY

  • BioCatalog (molecular biology softwares)
  • Codon usage of about 5000 organisms
  • Dana-Farber Cancer Institute Molecular Biology Core Facility
  • GCG manual
  • Intein database server (at NEB)
  • Restriction Enzyme Database REBASE (New England Biolab):

    • . Comprehensive Enzyme list

  • Vector-database at ATCG

  SEQUENCE ANALYSIS & PRESENTATION

  • Alscript 2.0 and some examples
  • AMAS - sequence alignment server by G. Barton; see also this page
  • BLAST from N.C.B.I.
  • BMERC - the PSA protein structure prediction server (Boston University)
  • BOXSHADE (Presentation of sequence alignment)
  • CATH - Protein structure classification
  • ExPasy and SwissProt
  • Multiple Sequence Alignment
  • National Center for Biotechnology Information (NCBI)
  • pI and M.W. (calculated)
  • ProSAL (Protein Sequence Analysis Launcher)
  • SeqAnalRef
  • Threader

  YEAST

  • Deletion Project and its search page
  • Gene-Chips.com
  • GeneStorm from Invitrogen
  • Introns
  • MicroArrayer at Pat Brown's lab and Botstein's Lab
  • Survey on microarray technology
  • Molecular Physiology of CNS development
  • Proteome Database
  • Saccharomyces Genome Database and its search SGD page
  • Yeast gene duplications
  • Yeast Lab Homepages
  • Yeast WWW virtual library

  Other Resources

  • Cold Spring Harbor Laboratory
  • Electronic cards
  • Educational Courses on the Web
  • Frontier in Biosciences: the Virtual Library
  • Ig Nobel Prize
  • Mapquest
    and its Driving directions
  • Lynx (vt100 Web browser); Updates
  • Nextwave from Science online
  • Nobel Foundation (Official web site)
    and its Electronic Nobel Museum Project
  • Textbooks (academic):
    
    • amazon.com
      
    • barnesandnoble.com
      
    • Polycrystal Book Service
      
    • TextbookHound.com
    • varsitybooks.com
      
  • World Health Organization (WHO)

  
  

  DATABASES SEARCHES

  • Computer Retrieval of Information on Scientific Projects (C.R.I.S.P.)
  • ExPASy and SwissProt
  • Litterature:
    • CARL which includes UnCover
    • Entrez
    • Institute for Scientific Information (ISI) and its Citation Reference Search (Also look at Web of science (part of Science Citation Index)
    • PubMed
  • Material Safety Data Sheets (searchable)
  • ModBase - Database of comparative protein structure models
  • Molecular Virology at the Univ. Wisconsin
  • National Center for Biotechnology Information (N.C.B.I.)
  • Restriction Enzyme Database: Comprehensive Enzyme list within REBASE
  • Sequence Retrival System (SRS5 at EMBL)
  • Web of science (part of Science Citation Index)

  
  

  DICTIONARIES AND REFERENCE RESOURCES

  • BIOSYS
  • Cell Biology
  • Elements of Style (English grammar)
  • Genetics (glossary)
  • HTML special characters
  • Internet terms (glossary)
  • Life Science
  • Mapquest and its Driving directions
  • Microbiology (glossary)
  • Patent server (IBM)
  • Periodic table at the University of British Columbia and at the Los Alamos National Laboratory
  • Phone directories: Canada and United States
  • Polycrystal Book Service
  • Thesaurus
  • Unix Help
  • Veterinary bacteriology - Dictionary (French)
  • Webster online

  
  

  JOURNALS

  • Acta Cryst. A Acta Cryst. D American Scientists Annual Reviews: Biochemistry Annual Rev: Biophys Biomol Struct Annual Reviews: Genetics Annual Reviews: Microbiology Annals of Improbable Research Antimicrob. Agents & Chemoth. Appl. Environ. Microbiol. Archive Microbiol. BBA: Gene Str. Express. BBA: Prot. Str. Mol. Enz. Biochemistry Biochem. & Cell Biology BioTechniques Biotechnol. & Bioengineering Blood Cell Cell. & Molec. Life Science Chemical & Eng. News Curr. Microbiol. Curr. Opin. Struct. Biol. EMBO J. Emerging Infectious Diseases Eur. J. Biochem. Eur. J. Immunol. FEMS Microbiol. Lett. Gene Genes & Development Genetics Genome Research Infection Immunity Intern. J. System. Bacteriol. J. Amer. Chem. Soc. J. Appl. Crystallography J. Bacteriology J. Biochemistry J. Biological Chemistry

    J. Cell Science J. Cellular Biochemistry J. Immunology J. Molecular Biology J. Structural Biology J. Synchrotron Radiation J. Virology Lancet Med. Microbiol. Immunol. Microbial Pathogenesis Microbiology Microbiol.Molec.Biol.Rev. Molec. Biol. of the Cell Molecular Cell Molecular & Cell. Biol. Molecular Microbiol. Nature Nature Biotechnology Nature Genetics Nature Medicine Nature Neuroscience Nature Structural Biology Nucleic Acid Research Physical Review Letters Pierce Proc. Natl Acad. Sci. USA Protein Engineering Protein Science Proteins: Struct.Funct.Genet. RNA Science Scientific American Soc.General Microbiol.Quart. Structure The Scientist Trends in Biochem. Sciences Trends in Genetics Trends in Microbiology Yeast

  - - - Instructions to authors - 2000 journals - - -
  
  Publishers and additional journal list sites:
  

  • Academic Press
  • American Society for Microbiology journals
  • Annual Reviews journals
  • BioMedNet Home Page
  • Biosciences at Harvard
  • Blackwell OnLine journals
  • Brandeis Library System:

    • Electronic Databases: A-F,   G-O  and   P-Z

      Main page of the libraries

      Search Louis database

  • CARL which includes UnCover
  • Entrez
  • IDEAL, online journals: guest login
  • Institute for Scientific Research (ISI) and its Citation Reference Search
  • Journal abbreviations
  • Journal list
  • National Cancer Institute -- Scientific Library
  • Pedro's list of Bio/Chemical Journals
  • PubMed
  • Royal Society - Publications
  • Sick Kids journal list
  • Web of science (part of Science Citation Index)
  • Wiley Intersciences

  
  

  NOMENCLATURE RECOMMENDED BY IUPAC AND IUBMB

  (Selected sections only)

  • Amino acids Bioorganic & bioinorganic     Carbohydrates Medicinal chemistry Nucleic acids sequences Organic chemistry

    Physical & organic chemistry Polypeptides Reactive intermediates Stereochemistry Steroids

  SOME SCIENTIFIC SOCIETIES

  • American Association for the Advancement of Science
  • American Association of Immunologists
  • American Cancer Society
  • American Chemical Society
  • American Crystallographic Association
  • American Society for Biochemistry and Molecular Biology
  • American Society for Cell Biology
  • American Society for Microbiology
  • Biochemical Society
  • Biophysical Society
  • British Society for Antimicrobial Chemotherapy
  • Canadian Federation of Biological Societies
  • European Federation of Biotechnology
  • Federation of American Societies for Experimental Biology
  • Federation of European Biochemical Societies
  • International Union of Biochemistry and Molecular Biology
  • International Union of Crystallography
  • International Union of Microbiological Societies
  • National Academy of Sciences
  • Pittsburgh Diffraction Society
  • Protein Society
  • Society for Developmental Biology
  • Society for Experimental Biology

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