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          EBIMED  Whaiizit  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              EBI  www.ebi.ac.uk/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/