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Useful Links for Structure-Function Lecture


SWBIC Educational Resources  >> Workshops  >> Bioinformatics  >> Readings

General

Molecular Biology Resources on the Web
http://www.med.nyu.edu/rcr/rcr/molbiolink.html
TransFac: The Transcription Factor Database
http://transfac.gbf.de/TRANSFAC/
The Eukaryotic Promoter Database
http://www.epd.isb-sib.ch/

Promoter finding programs on the Web

Promoter Scan: NIH Bioinformatics (BIMAS)
http://bimas.dcrt.nih.gov/molbio/proscan/
Promoter Scan II: Univ. of Minnesota & Axyx Pharmaceuticals
http://biosci.cbs.umn.edu/software/proscan/promoterscan.htm
Signal Scan: NIH Bioinformatics (BIMAS)
http://bimas.dcrt.nih.gov:80/molbio/signal/index.html
Transcription Element Search (TESS): Center for Bioinformatics, Univ. of Pennsylvania
http://www.cbil.upenn.edu/tess/
Search TransFac at GBF with MatInspector, PatSearch, and FunSiteP
http://transfac.gbf.de/programs.html
TargetFinder: Telethon Inst.of Genetics and Medicine, Milan, Italy
http://hercules.tigem.it/TargetFinder.html

Gene Finding programs on the Web

GRAIL: Oak Ridge Natl. Lab, Oak Ridge, TN
http://compbio.ornl.gov/Grail-1.3/
ORFfinder: NCBI
http://www.ncbi.nlm.nih.gov/gorf/gorf.html
DNA translation: Univ. of Minnesota Med. School
http://alces.med.umn.edu/webtrans.html
BCM GeneFinder: Baylor College of Medicine, Houston, TX
http://dot.imgen.bcm.tmc.edu:9331/seq-search/gene-search.html
http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html
Genome Web: Gene Identification Resources
http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-geneid.html

RNA folding programs on the Web

mfold version 3.0 by Zuker and Turner at Washington Univ. of St. Louis
http://mfold2.wustl.edu/~mfold/rna/form1.cgi
SStructView: RNA Secondary Structure Java Applet that visualizes RNA structures as calculated by mfold
http://smi-web.stanford.edu/projects/helix/pubs/gene-combis-96/eg-rnafold.html
RNA secondary structure prediction with GenBee at the Belozersky Institute, Moscow State University, Russia
http://www.genebee.msu.su/services/rna2_reduced.html
Protein Hydrophobicity Server: Bioinformatics Unit, Weizmann Institute of Science , Israel
http://bioinformatics.weizmann.ac.il/hydroph/
SAPS - statistical analysis of protein sequences
http://www.isrec.isb-sib.ch/software/SAPS_form.html

Protein Secondary Structure Prediction

Secondary Structural Content Prediction (SSCP): EMBL, Heidelberg
http://www.bork.embl-heidelberg.de/SSCP/sscp_seq.html
BCM Search Launcher: Protein Secondary Structure Prediction: Baylor College of Medicine
http://dot.imgen.bcm.tmc.edu:9331/seq-search/struc-predict.html
PREDATOR: EMBL, Heidelberg
http://www.embl-heidelberg.de/cgi/predator_serv.pl
UCLA-DOE Protein Fold Recognition Server
http://www.doe-mbi.ucla.edu/people/fischer/TEST/getsequence.html

"Super Secondary" Structures

Predict Protein server: : EMBL Heidelberg
http://www.embl-heidelberg.de/predictprotein/
Prediction of Transmembrane Regions & Orientation
http://www.ch.embnet.org/software/TMPRED_form.html
Prediction of Coiled Coil Regions in Proteins
http://www.www.ch.embnet.org/software/COILS_form.html
SignalP (signal peptides): Tech. Univ. of Denmark
http://www.cbs.dtu.dk/services/SignalP/

3D Structure Prediction

UCLA-DOE Protein Fold Recognition
http://www.doe-mbi.ucla.edu/people/fischer/TEST/getsequence.html
SwissModel: ExPASy, Univ. of Geneva
http://www.expasy.ch/swissmod/SWISS-MODEL.html
CPHmodels: Technical Univ. of Denmark
http://www.cbs.dtu.dk/services/CPHmodels/

Websites for PROSITE searches

ScanProsite at ExPASy: Univ. of Geneva
http://www.expasy.ch/tools/scnpsit1.html
Network Protein Sequence Analysis: Institut de Biologie et Chimie des Protéines, Lyon, France
http://pbil.ibcp.fr/NPSA/npsa_prosite.html
PPSRCH: EBI, Cambridge, UK
http://www2.ebi.ac.uk/ppsearch/

Protein Domain Databases

PFAM (1344 protein family HMM profiles built by hand): Washington Univ., St. Louis
http://pfam.wustl.edu/hmmsearch.shtml
ProDom (profiles built from PSI-BLAST automatic multiple alignments of the SwissProt database): INRA, Toulouse, France
http://www.toulouse.inra.fr/prodom/doc/blast_form.html

Websites for Profile searching

PROSITE ProfileScan: ExPASy, Geneva
http://www.isrec.isb-sib.ch/software/PFSCAN_form.html
BLOCKS (builds profiles from PROSITE entries and adds all matching sequences in SwissProt): Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
http://www.blocks.fhcrc.org/blocks_search.html
PRINTS
http://bioinf.man.ac.uk/dbbrowser/PRINTS/
MEME: San Diego Supercomputing Facility
http://www.sdsc.edu/MEME/meme/website/meme.html

Web links for the Phylogenetics Lecture

The Tree of Life project
http://phylogeny.arizona.edu/tree/phylogeny.html
Joseph Felsenstein (author of PHYLIP) maintains a comprehensive list of Phylogeny programs at:
http://evolution.genetics.washington.edu/phylip/software.html
Introduction to Phylogenetic Systematics,
Peter H. Weston & Michael D. Crisp, Society of Australian Systematic Biologists
http://www.science.uts.edu.au/sasb/WestonCrisp.html
University of California, Berkeley Museum of Paleontology (UCMP)
http://www.ucmp.berkeley.edu/clad/clad4.html

Phylogenetics servers on the web

The Institut Pasteur, Paris has a PHYLIP server at
http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html
The Belozersky Institute at Moscow State University in Russia has their own "GeneBee" phylogenetics server:
http://www.genebee.msu.su/services/phtree_reduced.html

 

 
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