BIOINFORMATICS: TOOLS AND RESOURCES

--- List of URLs ---

Monday 4 February

Bioinformatics Databases

EMBL (DNA sequence database)
http://www.ebi.ac.uk/embl/

ENTREZ (Search system for sequences and related information, at the NCBI in the States includes Medline)
http://www.ncbi.nlm.nih.gov/Entrez/

ExPASy (Comprehensive protein bioinformatics site, and one of the first in the world)
http://www.expasy.ch/

GDB (Mapping information for Human Genome Project)
http://www.gdb.org/

HGMD (Human Gene Mutation Database)
http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html

OMIM (Human genes and linked genetic disorders)
http://www.ncbi.nlm.nih.gov/Omim/

PubCrawler (Alerting service "It goes to the library, you go to the pub!")
http://www.gen.tcd.ie/pubcrawler/

The Sanger Centre, UK (Genome sequencing)
http://www.sanger.ac.uk/

SRS (Sequence search and retrieval system, at many sites worldwide this one's at the HGMP in Cambridge, UK)
http://srs.hgmp.mrc.ac.uk/

SRS worldwide public sites list
http://www.lionbio.co.uk/publicsrs.html

SwissProt and TrEMBL (Protein sequence databases)
http://www.expasy.ch/sprot/

TIGR (The Institute for Genetic Research, USA large scale gene sequencing and functional genomics)
http://www.tigr.org/

Software and Resources

The Human Genome Mapping Project Resource Centre (HGMP-RC)
http://www.hgmp.mrc.ac.uk/

EMBnet (general)
http://www.embnet.org/

IBB, Warsaw (Polish EMBnet node)
http://www.ibb.waw.pl/

EMBOSS (European Molecular Biology Open Software Suite)
http://www.uk.embnet.org/Software/EMBOSS/

JEMBOSS (Graphical user interface to EMBOSS)
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/


Tuesday 5 February

Protein Bioinformatics

BLAST at the NCBI
http://www.ncbi.nlm.nih.gov/BLAST/

ClustalW and Jalview at the EBI
http://circinus.ebi.ac.uk:6543/cgi-bin/clustalw.cgi

ProSite
http://www.expasy.ch/prosite/

PRINTS
http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

ProDom
http://prodes.toulouse.inra.fr/prodom/doc/prodom.html

Pfam
http://www.sanger.ac.uk/Software/Pfam/index.shtml

BLOCKS
http://www.blocks.fhcrc.org/

InterPro
http://www.ebi.ac.uk/interpro/

PIX [requires HGMP registration]
http://www.hgmp.mrc.ac.uk/Registered/Webapp/pix/


Wednesday 6 February

Genomes and Genome Projects

Nature's Genome Gateway
http://www.nature.com/genomics/

The Sanger Institute: Microbial Genomes
http://www.sanger.ac.uk/Projects/Microbes/

TIGR: Microbial Genomes
http://www.tigr.org/tdb/

Comprehensive Yeast Genome Database
http://mips.gsf.de/proj/yeast/CYGD/db/index.html

C. elegans Genome Project
http://www.sanger.ac.uk/Projects/C_elegans/

Arabidopsis Information Resource
http://www.arabidopsis.org/

FlyBase: A Database of the Drosophila Genome (at the EBI)
http://fly.ebi.ac.uk:7081/

NCBI's Human Genome Resources
http://www.ncbi.nlm.nih.gov/genome/guide/human/

GLIMMER (Bacterial/Archael gene finder)
http://www.tigr.org/softlab/glimmer/glimmer.html

GENSCAN (Eukaryotic gene finder)
http://genes.mit.edu/GENSCAN.html

NIX [requires HGMP registration]
http://www.hgmp.mrc.ac.uk/Registered/Webapp/nix/

Ensembl (human genome server)
http://www.ensembl.org/Homo_sapiens/

Artemis (genome annotation tool)
http://www.sanger.ac.uk/Software/Artemis/

ACT (genome comparison tool)
http://www.sanger.ac.uk/Software/ACT/

Protein Structure

The Protein Data Bank (PDB)
http://www.rcsb.org

Biological Macromolecule Crystallization Database (BMCD)
http://wwwbmcd.nist.gov:8080/bmcd/bmcd.html

Molecular Visualisation Freeware (Rasmol and Chime)
http://www.umass.edu/microbio/rasmol/

Structural Classification of Proteins (SCOP)
http://scop.mrc-lmb.cam.ac.uk/scop/

The CATH Protein Structure Classification
http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html

FSSP
http://www.ebi.ac.uk/dali/fssp/fssp.html

MRC-LMB: Max Perutz obituary
http://www2.mrc-lmb.cam.ac.uk/Max_Perutz.html


Thursday 7 February

Protein Modelling

Proteomics Tools at ExPASy
http://www.expasy.ch/tools/

Secondary Structure Prediction: Jpred / Jnet
http://jura.ebi.ac.uk:8888/

Transmembrane Helix Prediction: TMPred
http://www.ch.embnet.org/software/TMPRED_form.html

David Eisenberg's fold recognition server [Requires free login]
http://fold.doe-mbi.ucla.edu/

David Jones' fold recognition server (Threader)
http://bioinf.cs.ucl.ac.uk/psipred/

Mycobacterium tuberculosis structural genomics consortium homepage
http://www.doe-mbi.ucla.edu/TB/

Swiss-Model (free homology modelling server)
http://www.expasy.ch/swissmod/SWISS-MODEL.html

MODELLER (homology modelling)
http://guitar.rockefeller.edu/modeller/modeller.html

Whatif (relatively cheap, academic modelling program)
http://www.cmbi.kun.nl/whatif/

"O" (Mainly used in protein crystallography: can be used for modelling. Replaces the classic but obsolete Frodo)
http://imsb.au.dk/~mok/o/

Tripos (manufacturer of commercial modelling software: very expensive)
http://www.tripos.com/

Accelrys (Formerly MSI; as above)
http://www.accelrys.com/index.html

Procheck (for checking the quality of a structure or model)
http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

Verify-3D (David Eisenberg's web server for structure quality checking)
http://www.doe-mbi.ucla.edu/Services/Verify_3D/

The CASP protein structure prediction competitions
http://predictioncenter.llnl.gov/