Useful Links for Structure-Function Lecture

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


Molecular Biology Resources on the Web
TransFac: The Transcription Factor Database
The Eukaryotic Promoter Database

Promoter finding programs on the Web

Promoter Scan: NIH Bioinformatics (BIMAS)
Promoter Scan II: Univ. of Minnesota & Axyx Pharmaceuticals
Signal Scan: NIH Bioinformatics (BIMAS)
Transcription Element Search (TESS): Center for Bioinformatics, Univ. of Pennsylvania
Search TransFac at GBF with MatInspector, PatSearch, and FunSiteP
TargetFinder: Telethon Inst.of Genetics and Medicine, Milan, Italy

Gene Finding programs on the Web

GRAIL: Oak Ridge Natl. Lab, Oak Ridge, TN
ORFfinder: NCBI
DNA translation: Univ. of Minnesota Med. School
BCM GeneFinder: Baylor College of Medicine, Houston, TX
Genome Web: Gene Identification Resources

RNA folding programs on the Web

mfold version 3.0 by Zuker and Turner at Washington Univ. of St. Louis
SStructView: RNA Secondary Structure Java Applet that visualizes RNA structures as calculated by mfold
RNA secondary structure prediction with GenBee at the Belozersky Institute, Moscow State University, Russia
Protein Hydrophobicity Server: Bioinformatics Unit, Weizmann Institute of Science , Israel
SAPS – statistical analysis of protein sequences

Protein Secondary Structure Prediction

Secondary Structural Content Prediction (SSCP): EMBL, Heidelberg
BCM Search Launcher: Protein Secondary Structure Prediction: Baylor College of Medicine
PREDATOR: EMBL, Heidelberg
UCLA-DOE Protein Fold Recognition Server

“Super Secondary” Structures

Predict Protein server: : EMBL Heidelberg
Prediction of Transmembrane Regions & Orientation
Prediction of Coiled Coil Regions in Proteins
SignalP (signal peptides): Tech. Univ. of Denmark

3D Structure Prediction

UCLA-DOE Protein Fold Recognition
SwissModel: ExPASy, Univ. of Geneva
CPHmodels: Technical Univ. of Denmark

Websites for PROSITE searches

ScanProsite at ExPASy: Univ. of Geneva
Network Protein Sequence Analysis: Institut de Biologie et Chimie des Protéines, Lyon, France
PPSRCH: EBI, Cambridge, UK

Protein Domain Databases

PFAM (1344 protein family HMM profiles built by hand): Washington Univ., St. Louis
ProDom (profiles built from PSI-BLAST automatic multiple alignments of the SwissProt database): INRA, Toulouse, France

Websites for Profile searching

PROSITE ProfileScan: ExPASy, Geneva
BLOCKS (builds profiles from PROSITE entries and adds all matching sequences in SwissProt): Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
MEME: San Diego Supercomputing Facility

Web links for the Phylogenetics Lecture

The Tree of Life project
Joseph Felsenstein (author of PHYLIP) maintains a comprehensive list of Phylogeny programs at:
Introduction to Phylogenetic Systematics,
Peter H. Weston & Michael D. Crisp, Society of Australian Systematic Biologists
University of California, Berkeley Museum of Paleontology (UCMP)

Phylogenetics servers on the web

The Institut Pasteur, Paris has a PHYLIP server at
The Belozersky Institute at Moscow State University in Russia has their own “GeneBee” phylogenetics server: