Databases over Databases in Molecular Biology

SRS Sequence Retrieval System (network browser for databanks in molecular biology) http://www.embl-heidelberg.de/srs5/

Survey of Molecular Biology Databases and Servers

http://www.ai.sri.com/people/pkarp/mimbd/rsmith.html

BioMedNet Library

http://biomednet.com

DBGET Database Links

http://www.genome.ad.jp/dbget/dbget.links.html

Harvard Genome Research Databases and Selected Servers http://golgi.harvard.edu

Johns Hopkins Univ. OWL Web Server

http://www.gdb.org/Dan/proteins/owl.html

Index of Biology Internet Servers, USGS

http://info.er.usgs.gov/network/science/biology/index.html

Listing of Molecular Biology Databases (LiMB) gopher://gopher.nih.gov/11/molbio/other

WWW Server for Virology, UW-Madison

http://www.bocklabs.wisc.edu/Welcome.html

UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk/

WWW for the Molecular Biologists and Biochemists http://www.yk.rim.or.jp/~aisoai/index.html

Links to other Bio-Web servers

http://www.gdb .org/biolinks.html

Molecular Modelling Servers and Databases

http://www.rsc.org/lap/rsccom/dab/ind006links.htm

EMBO Practical Structural Databases

http://xray.bmc.uu.se/embo/structdb/links.html

Web Resources for Protein Scientists

http://www.faseb.org/protein/ProSciDocs/WWWResources.html

ExPASy Molecular Biology Server

http://expasy.hcuge.ch/cgi-bin/listdoc

The Antibody Resource Page

http://www.antibodyresource.com

Bioinformatics WWW Sites

http://biochem.kaist.ac.kr/bioinformatics.html

Bioinformatics and Computational Biology at George Mason University http://www.science.gmu.edu/~michaels/Bioinformatics/

INFOBIOGEN Catalog of Databases

http://www.infobiogen.fr/services/dbcat/

National Biotechnology Information Facility http://www.nbif.org/data/data.html

Human Genome Project Information

http://www.ornl.gov/TechResources/Human_Genome

Archives for biological software and databases

http://www.gdb.org/Dan/software/biol-links.html

Proteome Research: New Frontiers in Functional Genomics (book contents) http://expasy.hcuge.ch/ch2d/LivreTOC.html

13.4 Sequence and Structure Databases

13.4.1 Major Public Sequence Databases

EMBL WWW Services

http://www.EMBL-heidelberg.de/Services/index.html

GenBank Database Query Form (get a GenBank entry) http://ncbi.nlm.nih.gov/genbank/query_form.html

Protein Data Bank WWW Server (get a PDB structure) http://www.rcsb.org

European Bioinformatics Institute (EBI) http://www.ebi.ac.uk/

EBI Industry support

http://industry. ebi.ac .uk/

SWISS-PROT (protein sequences)

http://www.expasy.ch/sprot/sprot-top.html

PROSITE (functional protein sites)

http://expasy.hcuge.ch/sprot/prosite.html

Macromolecular Structures Database

http://BioMedNet.com/cgi-bin/members1/shwtoc.pl?J:mms

Molecules R Us (search and view a protein molecule) http://cmm.info.nih.gov/modeling/net_services.html

PIR-International Protein Sequence Database http://www.gdb.org/Dan/proteins/pir.html

SCOP (structural classification of proteins), MRC

http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.Lhtml

HIV Sequence Database, Los Alamos http://hiv-web.lanl.gov/

HIV Molecular Immunology Database, Los Alamos http://hiv-web.lanl.gov/immuno/index.html

TIGR Database

http://www.tigr.org/tdb/tdb.html

The NCBI WWW Entrez Browser

http://www.ncbi.nlm.nih.gov/Entrez/index.html

Cambridge Structural Database (small-molecule organic and organometallic crystal structures) http://www.ccdc.cam.ac.uk

Gene Ontology Consortium

http://genome-www.stanford.edu/GO/

13.4.2 Specialized Databases

ANU Bioinformatics Hypermedia Server

(virus databases, classification and nomenclature of viruses) http://life.anu.edu.au/

O-GLYCBASE (a revised database of O-glycosylated proteins) http://www.cbs.dtu.dk/OGLYCBASE/cbsoglycbase.html

Genome Sequence Database (GSDB) (relational database of annotated DNA sequences) http://www.ncgr.org

EBI Protein topology atlas

http://www3.ebi.ac.uk/tops/ServerIntermed.html

Database of Enzymes and Metabolic Pathways (EMP) http://www.empproject.com/

MAGPIE (multipurpose automated genome project investigation environment) http://www.mcs.anl.gov/home/gaasterl/magpie.html

E.coli database collection (ECDC) (compilation of DNA sequences of E. coli K12) http://susi.bio.uni-giessen.de/ecdc.html

Haemophilus influenzae database (HIDC) (genetic map, contigs, searchable index) http://susi.bio.uni-giessen.de/hidc.htm

EcoCyc: Encyclopedia of Escherichia coli Genes and Metabolism http://www.ai.sri.com/ecocyc/ecocyc.html

Eddy Lab snoRNA Database

http://rna.wustl.edu/snoRNAdb/

GenProtEc (genes and proteins of Escherichia coli) http://www.mbl.edu/html/ecoli.html

NRSub (non-redundant database for Bacillus subtilis) http://pbil.univ-lyon 1. fr/nrsub/nrsub.html

YPD (proteins from Saccharomyces cerevisiae) http://www.proteome.com/YPDhome.html

Saccharomyces Genome Database

http://genome-www.stanford.edu/Saccharomyces/

LISTA, LISTA-HOP and LISTA-HON (compilation of homology databases from yeast) http://www.ch.embnet.org/

FlyBase (Drosophila database) http://flybase.bio.indiana.edu/

MPDB (molecular probe database)

http://www.biotech.ist.unige.it/interlab/mpdb.html

Compilation of tRNA sequences and sequences of tRNA genes

http://www.uni-bayreuth.de/departments/biochemie/trna/index.html

Small RNA database, Baylor College of Medicine

http://mbcr.bcm.tmc.edu/smallRNA/smallrna.html

SRPDB (signal recognition particle database)

http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html

RDP (the Ribosomal Database Project) http://rdpwww.life .uiuc .edu/

Structure of small ribosomal subunit RNA http://rrna.uia.ac.be/ssu/index.html

Structure of large ribosomal subunit RNA http://rrna.uia. ac .be/lsu/index.html

RNA modification database

http://medlib.med.utah.edu/RNAmods/

HAMSTeRS (haemophilia A mutation database) and factor VIII mutation database http://europium.csc.mrc.ac.uk/usr/WWW/WebPages/main.dir/main.htm

Haemophilia B (point mutations and short additions and deletions) ftp://ftp.ebi.ac .uk/pub/databases/haemb/

Human p53, hprt and lacZ genes and mutations http://sunsite.unc .edu/dnam/mainpage.html

PAH mutation analysis (disease-producing human PAH loci) http://www.mcgill.ca/pahdb

ESTHER (cholinesterase gene server)

http://www.ensam.inra.fr/cgi-bin/ace/index

IMGT (immunogenetics database) http://www.ebi.ac .uk/imgt/

p53 mutations in human tumors and cell lines ftp://ftp.ebi.ac.uk/pub/databases/p53/

Androgen receptor gene mutations database ftp://www.ebi.ac.uk/pub/databases/androgen/

Glucocorticoid receptor resource

http://nrr.georgetown.edu/GRR/GRR.html

Thyroid hormone receptor resource

http://xanadu.mgh.harvard.edu//receptor/trrfront.html

16SMDB and 23SMDB (16S and 23S ribosomal RNA mutation database) http://www.fandm.edu/Departments/Biology/Databases/RNA.html

MITOMAP (human mitochondrial genome database) http://www.gen.emory.edu/mitomap.html

SWISS-2DPAGE (database of two-dimensional polyacrylamide gel electrophoresis) http://expasy.hcuge.ch/ch2d/ch2d-top.html

PRINTS (protein fingerprint database)

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/PRINTS/PRINTS.html

KabatMan (database of antibody structure and sequence information) http://www.bioinf.org.uk/abs/

ALIGN (compendium of protein sequence alignments)

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/ALIGN/ALIGN.html

CATH (protein structure classification system) http://www.biochem.ucl.ac.uk/bsm/cath/

ProDom (protein domain database) http://protein.toulouse.inra.fr/

Blocks database (system for protein classification) http://blocks.fhcrc.org/

HSSP (homology-derived secondary structure of proteins) http://www.sander.embl-heidelberg.de/hssp/

FSSP (fold classification based on structure-structure alignment of proteins) http://www2.ebi.ac.uk/dali/fssp/fssp.html

SBASE protein domains (annotated protein sequence segments) http://www.icgeb.trieste.it/~sbasesrv/

TransTerm (database of translational signals) http://uther.otago.ac.nz/Transterm.html

GRBase (database linking information on proteins involved in gene regulation) http://www.access.digex.net/~regulate/trevgrb.html

ENZYME (nomenclature of enzymes) http://www.expasy.ch/enzyme/

REBASE (database of restriction enzymes and methylases) http://www.neb.com/rebase/

RNaseP database

http://jwbrown.mbio.ncsu.edu/RNaseP/home.html

REGULONDB (database on transcriptional regulation in E. coli) http://www.cifn.unam.mx/Computational_Biology/regulondb/

TRANSFAC (database on transcription factors and their DNA binding sites) http://transfac.gbf.de/

MHCPEP (database of MHC-binding peptides) http://wehih.wehi.edu.au/mhcpep/

Mouse genome database

http://www.informatics.jax.org/mgd.html

Mouse knockout database

http://BioMedNet.com/cgi-bin/mko/mkobrwse.pl

ATCC (American type culture collection) http://www.atcc.org/

Histone sequence database of highly conserved nucleoprotein sequences http://www.ncbi.nlm.nih.gov/Baxevani/HISTONES

3Dee (database of protein structure domain definitions) http://barton.ebi.ac.uk/servers/3Dee.html

InterPro (integrated resource of protein domains and functional sites) http://www.ebi.ac .uk/interpro/

NRL_3D (sequence-structure database derived from PDB, pictures and searches) http://www.gdb.org/Dan/proteins/nrl3d.html

VBASE human variable immunoglulin gene sequences

http://www.mrc-cpe.cam.ac.uk/imt-doc/public/INTRO.html

GPCRD (G protein-coupled receptor data) http://www.gpcr.org/7tm/

Human Cytogenetics (chromosomes and karyotypes) http://www.selu.com/bio/cyto/human/index.html

Protein Kinase resource

http://www.sdsc.edu/projects/Kinases/pkr/pk_info.html#Format

Carbohydrate databases

http://www.boc.chem.ruu.nl/sugabase/databases.html

Borrelia Molecular Biology Home Page

http://www.pasteur.fr/Bio/borrelia/Welcome.html

Human papillomaviruses database http://HPV-web.lanl.gov/

Human 2-D PAGE databases for proteome analysis in health and disease http://biobase.dk/cgi-bin/celis

DBA mammalian genome size database

http://www.unipv.it/~webbio/dbagsh.htm

DOGS database Of Genome Sizes

http://www.cbs.dtu.dk/databases/DOGS/index.html

U.S. patent citation database

http://cos.gdb.org/repos/pat/

13.5 Sequence Similarity Searches

Sequence similarity search page at EBI

http://www.ebi.ac.uk/searches/searches.html

NCBI: BLAST notebook

http://www.ncbi.nlm.nih.gov/BLAST/

BLITZ ULTRA Fast Search at EMBL

http://www.ebi.ac.uk/searches/blitz_input.html

EMBL WWW services

http://www.embl-heidelberg.de/Services/index.html#5

Pattern scan of proteins or nucleotides

http://www.mcs.anl.gov/compbio/PatScan/HTML/patscan.html

MEME (motif discovery and search)

http://meme.sdsc.edu/meme/website/

CoreSearch (dentification of consensus elements in DNA sequences) http://www.gsf.de/biodv/coresearch.html

The PRINTS/PROSITE scanner (search motif databases with query sequence) http://www.biochem.ucl.ac.uk/cgi-bin/attwood/SearchPrintsForm.pl

DARWIN system at ETH Zurich http://cbrg.inf.ethz.ch/

PimaII find sequence similarity using dynamic programming http://bmerc-www.bu.edu/protein-seq/pimaII-new.html

DashPat find sequence similarity using a hashcode comparison with a pattern library http://bmerc-www.bu.edu/protein-seq/dashPat-new.html

PROPSEARCH (search based on amino acid composition, EMBL) http://www.embl-heidelberg.de/aaa.html

Sequence search protocol (integrated pattern search)

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/protocol.html

ProtoMap (automatic hierarchical classification of all swissprot proteins) http://www.protomap.cs.huji.ac.il/

GenQuest (Fasta, Blast, Smith Waterman; search in any database) http://www.gdb .org/D an/gq/gq.form.html

SSearch (searches against a specified database)

http://watson.genes.nig.ac.jp/homology/ssearch-e_help.html

Peer Bork search list (motif/pattern/profile searches) http://www.embl-heidelberg.de/~bork/pattern.html

PROSITE Database Searches (search for functional sites in your sequence) http://www.ebi.ac.uk/searches/prosite.html

PROWL—Protein Information Retrieval at Skirball Institute http://mcphar04.med.nyu.edu/index.html

CEPH genotype database

http://www.cephb.fr/cephdb/

13.6 Alignment

13.6.1 Pairwise Sequence and Structure Alignment

Pairwise protein alignment (SIM)

http://expasy.hcuge.ch/sprot/sim-prot.html

LALNVIEW alignment viewer program ftp ://expasy.hcuge. ch/pub/lalnview

BCM Search Launcher (pairwise sequence alignment)

http://searchlauncher.bcm.tmc.edu/seq-search/alignment.html

DALI compare protein structures in 3D http://www2 .ebi.ac .uk/dali/

DIALIGN (aligment program without explicit gap penalties) http://www.gsf.de/biodv/dialign.html

13.6.2 Multiple Alignment and Phylogeny

ClustalW (multiple sequence alignment at BCM)

http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html

PHYLIP (programs for inferring phylogenies)

http://evolution.genetics.washington.edu/phylip.html

Other phylogeny programs, a complication from PHYLIP documentation http://expasy.hcuge.ch/info/phylogen.sof

Tree of Life Home Page (information about phylogeny and biodiversity) http://phylogeny.arizona.edu/tree/phylogeny.html

Links for Palaeobotanists

http://www.uni-wuerzburg.de/mineralogie/palbot1.html

Phylogenetic analysis programs (the tree of life list)

http://phylogeny.arizona.edu/tree/programs/programs.html

Cladistics

http://www.kheper.auz.com/gaia/biosphere/systematics/cladistics.htm

Cladistic software (a list from the Willi Hennig Society) http://www.cladistics.org/education.html

BCM search launcher for multiple sequence alignments

http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html

AMAS (analyse multiply aligned sequences)

http://barton.ebi.ac.uk/servers/amas_server.html

Vienna RNA Secondary Structure Package http://www.tbi.univie. ac .at/~ ivo/RNA/

WebLogo (sequence logo)

http://www.bio.cam.ac .uk/cgi-bin/seqlogo/logo.cgi

Protein sequence logos using relative entropy

http://www.cbs.dtu.dk/gorodkin/appl/plogo.html

RNA structure-sequence logo

http://www.cbs.dtu.dk/gorodkin/appl/slogo.html

RNA mutual information plots

http://www/gorodkin/appl/MatrixPlot/mutRNA/

13.7 Selected Prediction Servers

13.7.1 Prediction of Protein Structure from Sequence

PHD PredictProtein server for secondary structure, solvent accesibility, and transmembrane segments

http://www.embl-heidelberg.de/predictprotein/predictprotein.html

PhdThreader (fold recognition by prediction-based threading) http://www.embl-heidelberg.de/predictprotein/phd_help.html

PSIpred (protein strcuture prediction server) http://insulin.brunel.ac.uk/psipred/

THREADER (David Jones)

http://www.biochem.ucl.ac.uk/~jones/threader.html

TMHMM (prediction of transmembrane helices in proteins) http://wwwcbs.dtu.dk/services/TMHMM/

Protein structural analysis, BMERC

http://bmerc-www.bu.edu/protein-seq/protein-struct.html

Submission form for protein domain and foldclass prediction http://genome.dkfz-heidelberg.de/nnga/def-query.html

NNSSP (prediction of protein secondary sturcture by nearest-neighbor algorithms) http://genomic.sanger.ac.uk/pss/pss.html

Swiss-Model (automated knowledge-based protein homology modeling server) http://www.expasy.ch/swissmod/SWISS-MODEL.html

SSPRED (secondary structure prediction with multiple alignment) http://www.mrc-cpe.cam.ac.uk/jong/predict/sspred.htm

SSCP (secondary structure prediction content with amino acid composition) http://www.mrc-cpe.cam.ac.uk/jong/predict/sscp.htm

SOPM (Self Optimized Prediction Method, secondary structure) at IBCP, France. http://pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopm.html

NNPREDICT (neural network for residue-by-residue prediction) http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html

SSpro (secondary structure in 3 classes) http://promoter.ics.uci.edu/BRNN-PRED/

SSpro8 (secondary structure in 8 classes) http://promoter.ics.uci.edu/BRNN-PRED/

ACCpro (solvent accessibility)

http://promoter.ics.uci.edu/BRNN-PRED/

CONpro (contact number)

http://promoter.ics.uci.edu/BRNN-PRED/

TMAP (service predicting transmembrane segments in proteins) http://www.embl-heidelberg.de/tmap/tmap_info.html

TMpred (prediction of transmembrane regions and orientation) http://www.ch.embnet.org/software/TMPRED_form.html

MultPredict (secondary structure of multiply aligned sequences) http://kestrel.ludwig.ucl.ac.uk/zpred.html

NIH Molecular Modeling Homepage (modelling homepage with links) http://cmm.info.nih.gov/modeling/

BCM Search Launcher (protein secondary structure prediction)

http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html

COILS (prediction of coiled coil regions in proteins)

http://www.ch.embnet.org/software/coils/COILS_doc.html

Coiled Coils

http://www.york.ac.uk/depts/biol/units/coils/coilcoil.html

Paircoil (location of coiled coil regions in amino acid sequences) http://theory.lcs.mit.edu/bab/webcoil.html

PREDATOR (protein secondary structure prediction from single sequence) http://www.embl-heidelberg.de/argos/predator/predator_info.html

DAS (Dense Alignment Surface; prediction of transmembrane regions in proteins) http://www.biokemi.su.se/~server/DAS/

Fold-recognition at UCLA-DOE structure prediction server http://www.doe-mbi.ucla.edu/people/frsvr/frsvr.html

Molecular Modelling Servers and Databases

http://bionmr5.bham.ac.uk/modelling/model.html

EVA (automatic evaluation of protein structure prediction servers) http://cubic.bioc.columbia.edu/eva/

13.7.2 Gene Finding and Intron Splice Site Prediction

NetGene (prediction of intron splice sites in human genes) http://www.cbs.dtu.dk/services/NetGene2/

NetPlantGene (prediction of intron splice sites in Arabidopsis thaliana) http://www.cbs.dtu.dk/services/NetPGene

GeneQuiz (automated analysis of genomes)

http://www.sander.embl-heidelberg.de/genequiz/

GRAIL interface (protein coding regions and functional sites) http://avalon.epm.ornl.gov/Grail-bin/EmptyGrailForm

GENEMARK (WWW system for predicting protein coding regions) http://genemark.biology.gatech.edu/GeneMark

GENSCAN Web Server: Complete gene structures in genomic DNA http://gnomic.stanford.edu/~chris/GENSCANW.html

FGENEH Genefinder: Prediction of gene structure in human DNA sequences http://mbcr.bcm.tmc.edu/Guide/Genefinder/fgeneh.html

GRAIL and GENQUEST (E-mail sequence analysis, gene assembly, and sequence comparison)

http://avalon.epm.ornl.gov/manuals/grail-genquest.9407.html

CpG islands finder

http://www.ebi.ac.uk/cpg/

Eukaryotic Pol II promoter prediction

http://biosci.umn.edu/software/proscan.html

Promoter prediction input form

http://www-hgc.lbl.gov/projects/promoter.html

Web Signal Scan Service (scan DNA sequences for eukaryotic transcriptional elements) http://bimas.dcrt.nih.gov/molbio/signal/

Gene Discovery Page

http://konops.imbb.forth.gr/~topalis/mirror/gdp.html

List of genome sequencing projects

http://www.mcs.anl.gov/home/gaasterl/genomes.html

13.7.3 DNA Microarray Data and Methods

Cyber-T (DNA microarray data analysis server) http://128.200.5.223/CyberT/

Brown Lab guide to microarraying http://cmgm.stanford.edu/pbrown

Stanford Microarray Database

http://genome-www4.stanford.edu/MicroArray/SMD/

Stanford MicroArray Forum

http://cmgm.stanford.edu/cgi-bin/cgiwrap/taebshin/dcforum/dcboard.cgi

Brazma microarray page at EBI

http://industry.ebi.ac.uk/~brazma/Data-mining/microarray.html

Web resources on gene expression and DNA microarray technologies http://industry. ebi.ac .uk/~ alan/MicroArray/

Gene-X (array data management and analysis system) http://www.ncgr.org/research/genex/

UCI functional genomics array tools and software http://www.genomics.uci.edu/

Matern's DNA Microarray Page

http://barinth.tripod.com/chips.html

Public source for microarraying information, tools, and protocols http://www.microarrays.org/

Weisshaar's listing of DNA microarray links

http://www.mpiz-koeln.mpg.de/~weisshaa/Adis/DNA-array-links.html

DNA microarray technology to identify genes controlling spermatogenesis http://www.mcb.arizona.edu/wardlab/microarray.html

13.7.4 Other Prediction Servers

NetStart (translation start in vertebrate and A. thaliana DNA) http://www.cbs.dtu.dk/services/NetStart/

NetOGlyc (O-glycosylation sites in mammalian proteins) http://www.cbs.dtu.dk/services/NetOGlyc/

YinOYang (O-^-GlcNAc sites in eukaryotic protein sequences) http://www.cbs.dtu.dk/services/YinOYang/

SignalP

(signal peptide and cleavage sites in gram+, gram-, and eukaryotic proteins) http://www.cbs.dtu.dk/services/SignalP/

NetChop (cleavage sites of the human proteasome) http://www.cbs.dtu.dk/services/NetChop/

NetPhos (serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins) http://www.cbs.dtu.dk/services/NetPhos/

TargetP (prediction of subcellular location) http://www.cbs.dtu.dk/services/TargetP/

ChloroP (chloroplast pransit peptide prediction) http://www.cbs.dtu.dk/services/SignalP/

PSORT (prediction of protein-sorting signals and localization from sequence) http://psort.nibb.ac.jp/

PEDANT (prtein extraction, description, and analalysis tool) http://pedant.mips.biochem.mpg.de/

Compare your sequence to COG database

http://www.ncbi.nlm.nih.gov/COG/cognitor.html

Prediction of HLA-binding peptides from sequences

http://www-bimas.dcrt.nih.gov/molbio/hla_bind/index.html

13.8 Molecular Biology Software Links

Visualization for bioinformatics

http://industry.ebi.ac.uk/ alan/VisSupp/

The EBI molecular biology software archive

http://www.ebi.ac.uk/software/software.html

The BioCatalog

http://www.ebi.ac.uk/biocat/e-mail_Server_ANALYSIS.html

Archives for biological software and databases

http://www.gdb.org/Dan/softsearch/biol-links.html

Barton group software (ALSCRIPT, AMPS, AMAS, STAMP, ASSP, JNET, and SCANPS) http://barton.ebi.ac.uk/new/software.html

Cohen group software rotamer library, BLoop, QPack, FOLD, Match, http://www.cmpharm.ucsf.edu/cohen/pub/

Bayesian bioinformatics at Wadsworth Center http://www.wadsworth.org/res&res/bioinfo/

Rasmol software and script documentation http://scop.mrc-lmb.cam.ac.uk/std/rs/

MolScript

http://ind1.mrc-lmb.cam.ac.uk/external-file-copies/molscript.html

WHAT IF

http://www.hgmp.mrc.ac.uk/Registered/Option/whatif.html

Biosym (Discover)

http://ind1.mrc-lmb.cam.ac.uk/external-file-copies/biosym/ discover/html/Disco_Home.html

SAM software for sequence consensus HMMs at UC Santa Cruz http://www.cse.ucsc.edu/research/compbio/sam.html

HMMER (source code for hidden Markov model software) http://hmmer.wustl.edu/

ClustalW

http://www.ebi.ac .uk/clustalw/

DSSP program

http://www.sander.embl-heidelberg.de/dssp/

Bootscanning for viral recombinations

http://www.bio.net//hypermail/RECOMBINATION/recom.199607/0004.html

Blocking Gibbs sampling for linkage analysis in very large pedigrees http://www.cs.auc.dk/~claus/block.html

ProMSED (protein multiple sequences editor for Windows) ftp://ftp.ebi.ac.uk/pub/software/dos/promsed/

DBWatcher for Sun/Solaris

http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/

ProFit (protein least squares fitting software) http://www.bioinf.org.uk/software/

Indiana University IUBIO software and data http://iubio .bio.indiana.edu/

Molecular biology software list at NIH http://bimas.dcrt.nih.gov/sw.html

ProAnalyst software for protein/peptide analysis ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst/

DRAGON protein modelling tool using distance geometry

http://www.nimr.mrc.ac.uk/~mathbio/a-aszodi/dragon.html

Molecular Surface Package

http://www.best.com/~connolly/

Biotechnological Software and Internet Journal http://www.orst.edu/~ahernk/bsj.html

MCell (Monte Carlo simulator of cellular microphysiology) http://www.mcell.cnl.salk.edu/

HHMpro (HMM simulator for sequence analysis with graphical interface) http://www.netid.com/html/hmmpro.html

13.9 Ph.D. Courses over the Internet

Biocomputing course resource list: course syllabi

http://www.techfak.uni-bielefeld.de/bcd/Curric/syllabi.html

Ph.D. course in biological sequence analysis and protein modeling http://www.cbs.dtu.dk/phdcourse/programme.html

The Virtual School of Molecular Sciences

http://www.ccc.nottingham.ac.uk/vsms/sbdd/

EMBnet Biocomputing Tutorials

http://biobase.dk/Embnetut/Universl/embnettu.html

Collaborative course in protein structure

http://www.cryst.bbk.ac.uk/PPS/index.html

GNA's Virtual School of Natural Sciences

http://www.techfak.uni-bielefeld.de/bcd/Vsns/index.html

Algorithms in molecular biology

http://www.cs.washington.edu/education/courses/590bi/

ISCB education working group

http://www.sdsc.edu/pb/iscb/iscb-edu.html

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