General Tools pages

HTML Authoring Tools

EXPASY- The SWISS Protein Bioinformatics Institute home page: for protein analysis and proteomics tools

EBI The European Bioinformatics institute site for sequence analysis services

The Sanger Centre for links to bacterial, human, yeast, parasite and the C. elegans genome projects.

NCBI - the home of GenBank, and of database query, retrieval and sequence search using BLAST

see BCM Search Launcher at http://kiwi.imgen.bcm.tmc.edu:8088/searchlauncher/launcher.html for additional tools

Finding sequences in public databases

ENTREZ at http://www.ncbi.nlm.nih.
gov/Entrez/

SRS at http://srs.ebi .ac.uk/

dbEST at http://www.ncbi.nlm.nih.
gov/dbEST/index.html

SWISSPROT is available through http://www.expasy.
ch/sprot/

Database Searching

BLAST searches at http://www .ncbi.nlm .nih.gov/
BLAST/

BLAST2 is at http://www.ncbi.
nlm.nih.gov/
cgi-bin/BLAST/
nph-newblast?Jform=1

PSI-BLAST is at http://www.ncbi.
nlm.nih.gov/
cgi-bin/ BLAST/
nph-psi_blast

The TIGR database search engines are accessible through http://www.t igr.org/

EBI Blast searches http://www2.ebi.ac.uk/
blast2/ [FASTA searches at http://www2. ebi.ac.uk/
fasta3/]

Sequence Search Site at http://sss.stanford
.edu/sss/

The Sanger Centre genome sequencing teams have specific search engines for each project, see http://www. sanger.ac.uk/

Caenorhabditis elegans specific searches at http://www. sanger.ac.uk/
Projects/C_ elegans/ blast_server.shtml

Genome Computing/ Bioinformatics centres

EUROPEAN BIOINFORMATICS INSTITUTE http://www.ebi.ac.uk/
cgi-bin/rbanner/
index.cgi

SANGER CENTRE http://www.sanger.ac.uk/

WASHINGTON UNIVERSITY GENOME CENTRE http://www.gsc.wustl.edu/

THE INSTITUTE FOR GENOME RESEARCH http://www. tigr.org/

Multiple alignment tools on the WWW

CLUSTALW at the EBI at http://www2.ebi.ac.uk/
clustalw

Multiple alignment tool
http://dot.imgen. bcm.tmc.edu:9331/ multi-align/ multi-align.html

see BCM Search Launcher at http://kiwi.imgen.bcm.
tmc.edu:8088/searchlauncher/
launcher.html for additional tools

Profile and HMM search tools

HMMer at http://hmmer.wustl.edu/

BLOCKs search tools at http://www.blocks. fhcrc.org/

Pfam HMM scan at http://www. sanger.ac.uk/
Software/Pfam/

Pfam HMM scan at http://pfam. wustl.edu/

Protein Analysis

PROSITE pattern scans at http://www.expasy.ch/
sprot/ scnpsit1.html

PROSITE profile scans at http://www. isrec.isb-sib.ch/
software/
PFSCAN _form.html

PROSITE frame-tolerant profile scans at http://www.isrec.
isb-sib.ch/
software/
PFRAMESCAN _form.html

PRINTS database and searches at http://www.biochem.
ucl.ac.uk/
bsm/ dbbrowser / PRINTS/

see here for a link to the EXPASY/ SWISSPROT protein analysis site

PSORT: prediction of where in the cell a protein may be targetted: PSORT at psort.nibb.ac.jp

Prediction of transmembrane segments: TMPRED at tmpred http://www .isrec.isb-sib.ch/

(see here for a comment on this)

SignalP server at http://www.cbs.dtu.dk/services/SignalP/

Translate DNA on the WWW with links to peptide analysis servers at EXPASY using http://www.expasy.ch/tools/dna.html

Structure Databases

SCOP at http://scop. mrc-lmb.cam.
ac.uk/scop/

CATH at http://www.biochem.
ucl.ac.uk/
bsm/cath/

Restriction enzymes

New England Biolabs REBASE at http://www.neb.com/ rebase/rebase.htm

Cut your DNA online at http://www. ccsi.com/ firstmarket/cutter