Links to affiliated groups and relevant material

♣ Embedded core initiatives CMSB - The Dutch Centre for Medical Systems Biology DIAL - CMSB Data Integration, Analysis and Logistics Dutch national Ecogenomics project NBIC - Netherlands Bioinformatics Centre Dutch national BioRange project ♣ Collaborations NIMR Mathematical Biology Department VU Molecular Cell Physiology Department ♣ Online Journals PubMed, database of journals Bioinform Bioinformatics Computers and Chemistry In Silico Biology Journal of Computational Biology Journal of Molecular Biology (JMB) Nature Nature Genome Gateway Nucleic Acids Research (NAR) Protein Science Proteins: Structure Function and Genetics Science The Bioinformer, published by EBI Trends in Biochemical Sciences (TiBS) ♣ Database Searching BLAST Server - Sequence searches at NCBI Database searches - Similarity & Homology searching at EBI Database searches at DISC (Japan) - Includes Fasta, BLAST, MPsrch and SRS Fasta Entrez - Browse a subset of MEDLINE, and the NCBI protein and nucleotide databases Match sequence against PROSITE ♣ Other Bioinformatics Resources BIBISERV - Bielefeld University Bioinformatics Server ExPASy - Proteomics server Human Genome Project Information

♣ Bioinformatics Centers EBI - European Bioinformatics Institute EMBL - European Molecular Biology Laboratory NCBI - National Center for Biotechnology Information CBS - Center for Biological Sequence Analysis, Technical University of Denmark BSM - Biomolecular Structure and Modelling at UCL Sanger centre, Hinxton, England DDBJ - DNA data bank, Japan HUM-MOLGEN - Human Molecular Genetics Centre of Bioinformatics, Peking ♣ Multiple Sequence Alignment MUSCLE - Multiple sequence alignment T-COFFEE - Multiple sequence alignment dbClustal - Multiple sequence alignment (part of PipeAlign track) Clustal W - Multiple sequence alignment SAM - Sequence alignment and modeling system (using HMMs) AMAS - Analysis of multiple alignments (Geoff Barton) HMMER - Multiple sequence alignment DIALIGN 2 - Multiple sequence alignment ♣ Secondary Structure Prediction PredictProtein - Server to predict protein structure PSI-Pred - PSI-BLAST-based protein secondary structure prediction ♣ Modelling and Data analysis DALI - Comparison of protein structures in 3D Pratt - Pattern discovery online Expression Profiler - Online tool for expression profile clustering and sequence pattern discovery PSA - Protein Sequence Analysis: fits a structure model to your sequence Block Maker - At Fred Hutchinson Cancer Research Center MEME - Multiple EM for Motif Elicitation