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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


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