Links for servers and software for Bioinformatics courses for students at University of Bern
Main Portals: NCBI www.ncbi.nlm.nih.gov
EBI www.ebi.ac.uk
UniProt/SwissProt www.uniprot.org
Genomes UCSC Genome Browser NCBI Map Viewer
Yeast Genome Microbial Genomes
FlyBase http://flybase.bio.indiana.edu/
WormBase http://www.wormbase.org
TAIR http://www.arabidopsis.org/
Literature: PUBMED www.ncbi.nlm.nih.gov/pubmed Science Citation Index
OMIM http://www3.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
BIND http://www.blueprint.org/bind/bind.php
GO http://www.geneontology.org/
BLAST servers: NCBI www.ncbi.nlm.nih.gov/blast
EMBNet www.expasy.ch/blast
BLAT Search for Genomes BLAT
Seq alignment Blast2Seq Lalign TCoffee ClustalW
Sequence conversion: ReadSeq
Alignment Editors GeneDoc CINEMA BOXSHADE JALVIEW
CLC Sequence Viewer (Very good tool for local install)
DNA Seq Analysis BioTools NEBcutter Sequence Editor Nucleic Acid Sequence Massager
Feature Extractor ORF Finder VectorScreen
Prot Seq Analysis ProtParam tool (Physical and Chemical Properties of a given Protein Sequence)
Peptide Cutter (Digestion of Proteins)
PIR http://pir.georgetown.edu/ MIPS http://mips.gsf.de/
UniProt http://www.uniprot.org/
Protein family PROSITE http://www.expasy.org/prosite/
PRINTS http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
Blocks http://blocks.fhcrc.org/
Profiles http://hits.isb-sib.ch/cgi-bin/PFSCAN/
Pfam http://www.sanger.ac.uk/Software/Pfam/
eMOTIF http://fold.stanford.edu/emotif/
InterPro http://www.ebi.ac.uk/interpro/
Protein structure PDB http://www.rscb.org/pdb/
SCOP http://scop.mrc-lmb.cam.ac.uk/scop/
CATH http://www.biochem.ucl.ac.uk/bsm/cath/
PDBsum http://www.biochem.ucl.ac.uk/bsm/pdbsum/
CDD http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
3D Str Prediction Swiss Model HHPRED
Metabolic/pathway KEGG http://www.genome.ad.jp/
WIT http://www-wit.mcs.anl.gov/Gongxin/
EcoCyc http://ecocyc.org/
UMBBD http://umbbd.ahc.umn.edu/