directory of resources for molecular biology and bioinformatics.

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Links and Resources

The following list is a directory of resources for molecular biology and bioinformatics. This site was compiled by Monique Meloche and Brenda Muskat.

Please send any useful bioinformatics sites to monique

 

 

Major Biotechnology Centres

Bioinformatics Research Centres

Organismal Databases 2D and 3D Structures Sequence Analysis

Molecular Evolution

Metabolic Function Bioinformatics Degree and Certificate Programs

 

 

Bioinformatics

 

 

WEIZMANN INSTITUTEThe Bioinformatics Unit and Genome Resource Core (BIGROC) at the Weizmann Institute of Science. This centre's focus is in design and development of tools for Bioinformatics, especially in the areas of Molecular Biology and Genome Analysis. BASE4 INCBase4 applies advanced bioinformatic analysis to identify commercially valuable genes on which it establishes strong, proprietary positions.

Major Biotechnology Centres

European Bioinformatics Institute (EMBL) European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures. ExPASyThis is the ExPASy World Wide Web (WWW) molecular biology server of the Geneva University Hospital and the University of Geneva. This server is dedicated to the analysis of protein and nucleic acid sequences as well as 2-D PAGE. KEGGKyoto Encyclopedia of Genes and Genomes (KEGG) maintains current knowledge of molecular and cellular biology information pathways. The KEGG project is being undertaken in the Institute for Chemical Research, Kyoto University as part of the

Japanese Human Genome Program. NCBI Nat! ional Center for Biotechnology Information. THE SANGER CENTRE HOME PAGEThe Sanger Centre is a new research centre established jointly by the Wellcome Trust and the British Medical Research Council to provide a major focus in the UK for mapping and sequencing the human genome, and genomes of other organisms. NCBI National Center for Biotechnology InformationMicroarray Centre at The Ontario Cancer InstituteThe Microarray Centre at The Ontario Cancer Institute is a leader in Canadian microarray technology. We are dedicated to providing high quality microarrays, technical support and service to Canadian researchers. Access to high quality microarrays will allow our

Canadian researchers to be on the cutting edge of genetic research.

Organismal Databases

 

Caenorhabditis elegansEcherichia coliHaemophilus influenzaeHuman - The Genome DatabaseMaizeMouse - The Jackson LaboratorySalmonella typhimuriumSaccharomyces cerevisiaeTetrahymena

2D and 3D structure

FoldBiomolecular Modelling LaboratoryImage Library of Biological MacromoleculesThree-dimensional biopolymer structures with an emphasis on visualization and analysis Protein MotionDatabase of macromolecular movements including motions of loops, domains, and subunits.NRL 3DThe NRL_3D database is produced by PIR from sequence and annotation information extracted from the Brookhaven Protein Databank (PDB) of crystallographic structures.Swiss-Model: Automated Protein

Modelling ServerSwiss-Model is an Automated Prot! ein Modelling Server running at the Geneva Biomedical Research Institute, Glaxo Wellcome Research and Development S.A., Switzerland.

Sequence Analysis

AA Analysis Protein Identification in SwissProt and PIR using Amino Acid Composition at EMBL-Heidelberg.AA CompIdent Searches SWISS-PROT for proteins whose amino acid compositions are closest to the given composition. AACompSim Compare the amino acid composition of a SWISS-PROT entry with all other entries. BLOCKS A searchable database of highly conserved protein domains. You can search, create, and retrieve blocks.BLITZ (BIC-SW)Performs fast, sensitive alignments of your protein

against those in Swiss-Prot (Smith and Waterman algorithm). CombSearch An experimental unified interface to query several protein identification tools accessible on the web. Compute pi/Mw Compute the theoretical pi and Mw from a SWISS-PROT or TrEMBL entry or from a user-entered sequence. FindMod Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified SWISS-PROT entry or from a user-entered sequence, and mass differences are used to better characterise the protein of interest. Mascot Peptide Mass Fingerprint, Sequence Query and MS/MS Ion Search from Matrix Science Ltd., ! London. MultiIdent Identify proteins with pI, Mw, amino acid composition, sequence tag, and peptide mass fingerprinting data.PeptIdent Identify proteins with peptide mass fingerprinting data, pi and Mw. Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in SWISS-PROT, making extensive use of database annotations. PeptideMass Calculate masses of peptides and their post-translational modifications for a SWISS-PROT or TrEMBL entry or from a user-entered sequence. PeptideSearch Peptide mass fingerprint tool from EMBL Heidelberg. Pfam A searchable database of aligned protein domains. You can also retrieve entire families. PredictProtein A server to perform various database searches and predict aspects of protein structure. PRINTSProtein Motif Fingerprints Database. ProDom A searchable database of homologous protein domains/families. Based on recursive PSI-BLAST searches. PROPSEARCH Identify functional/structural homologs of your protein based on protein properties, not alignments. PROSITE A searchable database of protein families and domains that will iden! tify matches in your protein to PRProteinProspector A variety of tools from UCSF (MS-Fit, MS-Tag, MS-Digest, etc.) for mining sequence databases in conjunction with mass spectrometry experiments [Mirror at UCL-Ludwig, UK]. PROWLProtein chemistry and mass spectrometry resource from Rockefeller and NY Universities.SMARTWill run your protein sequence through a multiple domain databases simultaneously. TagIdent Identify proteins with pi, Mw, and sequence tag, or generate a list of proteins close to a given pi and Mw. TM FinderDeveloped by Dr. Charles Deber, TM Finder uses this experimentally-deriv! ed information in specific combinations to identify the "transmembrane" segments in membrane proteins.

 

Molecular Evolution

PHYLOGENETIC ANALYSIS PROGRAMSAn extensive guide to phylogenetic analysis programs including: tree inferences, alignment, character and tree analysis. PHYLIP A package of programs for evolutionary genetics and phylogenetic analysisTREE GENTree generation from distance data. TREE OF LIFE Phylogeny and biodiversity database containing information about the diversity of organisms on Earth, their history, and characteristics. The information is linked together in the form of the evolutionary tree that connects all

organisms to each other.

 

Metabolic Functions

KEGGMetabolic and regulatory pathway database providing extensive pathway maps and ortholog tables.WIT Interactive metabolic reconstruction programs. Curation of function assignments made to genes and the development of metabolic modelsMetabolic DatabaseThe metabolic component of SoyBase, a soybean genetic database, contains reaction and pathway descriptions and diagrams for a number of basic metabolic pathways

 

 

 

Bioinformatics University Programs

BOSTON UNIVERSITYProvides a graduate program in Bioinformatics offereing both M.Sc. and Ph.D. degrees. A number of different departments are involved in this program.

JOHNS HOPKINSDepartment of Information Science and the The Welch Laboratory for Applied Bioinformatics offer both M.Sc. and Ph.D. programs related to computational biology but not specifically in Bioinformatics.

RUTGERS AND THE UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEYGraduate studies in computational molecular biology offer a Ph.D. degree. Training involves a variety of fields including bioinformatics, genomics, molecular evolution, macromolecular structure, dynamics and function, pattern recognition and, image analysis.

STANFORD CENTER FOR PROFESSIONAL DEVELOPMENTCertificate program in Bioinformatics consisting of a three-course series. Courses included are: computational molecular biology, protein architecture, representational and algorithms for computational molecular biology.

STANFORD UNIVERSITYThe Brutlag Group affiliated with the Stanford Medical Informatics School. Offers both graduate programs and postdoctoral fellowships.

UNIVERSITY OF CALIFORNIA, LOS ANGELESBioinformatics graduate program offering a Ph.D. degree. Interdisciplinary program with students from multiple departments creating an organizing center.

UNIVERSITY OF CALIFORNICA, SANTA CRUZBaskin Center for Computer Science and Engineering. Program in Medical Information Science (Bioinformatics) offering both M.Sc. and Ph.D. degrees.UNIVERSITY OF PENNSYLVANIAInstitute of Medicine and Engineering offering B.Sc., M.Sc. and Ph.D. degrees in Computational Biology and Bioinformatics.

UNIVERSITY OF WATERLOOAn interdisciplinary Bioinformatics co-op program. The Bioinformatics program has three routes leading to the following degrees: B.Sc (Honours Bioinformatics), B.Math (Honour Compute Sciences - Bioinformatics), B.Sc (Honours Biology and Bioinformatics).WASHINGTON UNIVERSITYDivision of Biology, Biomedical Sciences and, Biomedical Engineering departments. Program leads to a Ph.D. in bioinformatics and Computational molecular biology. This program targets students with a biological and experimental background

interested in integrating computational studies.

W. M. KECK CENTRE (PITTSBURGH)Center for Computational Biology in Pittsburgh, Pennsylvania. A collaboration between Carnegie Melon, the Pittsburgh Supercomputing Centre, and the University of Houston. The center provides graduate and postdoctoral training in computational biology through other formal programs of study.

W. M. KECK CENTRE A joint venture between Baylor College of Medicine, Rice University, and the University of Houston. Training for graduates and postdoctoral fellows in Bioinformatics and Computational Biology. This program is supported by the National Library of Medicine and The National Science Foundation.

 

 

 

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