CENTER for MOLECULAR MEDICINE & GENETICS

Wayne State University School of Medicine

MBG 8680: Computer Applications in Molecular Genetics

[MBG 8680 Home Page]

SOME VERY USEFUL INTERNET SITES

DATABASES

EMBL

European Molecular Biology Laboratory
http://www.ebi.ac.uk/
http://www.ebi.ac.uk/proteome/

Ensembl

Human Genome Server
http://www.ensembl.org/genome/central/
http://www.ensembl.org/

NCBI

National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/

GEO

NCBI Gene Expression Omnibus
http://www.ncbi.nlm.nih.gov/geo/

SOURCE

Stanford Online Universal Resource for Clones and ESTs
http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch

UCSC Genome Bioinformatics Site

This site contains the reference sequence for the human genome and working drafts for the mouse, rat, and SARS genomes.
http://genome.ucsc.edu/

Transcription Factor Database

Keep your transcription factor data files up to date with the latest version of tfsites.dat from the Institute for Transcriptional Informatics (IFTI).
http://www.accelrys.com/products/dstudio/gene/freebies.html

iHOP: What is the biology of my sequence?

Information Hyperlinked Over Proteins.
http://www.ihop-net.org/UniPub/iHOP/

Vista Viewer

Conserved Noncoding Sequences that Control Expression
http://genome.lbl.gov/vista/index.shtml

SOFTWARE

Multi-Function

EMBOSS is a package of high-quality FREE Open Source software for sequence analysis
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/

EMBOSS GUI via National Research Council of Canada
http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html

Staden Package
http://www.mrc-lmb.cam.ac.uk/pubseq/staden_home.html

Gene Annotation

Genotator
http://www.fruitfly.org/~nomi/genotator/

PANORAMA, POMPOUS and PRIMO (3P) Server
http://atlas.swmed.edu/

Computational Biology at Oak Ridge National Laboratory
http://compbio.ornl.gov/tools/index.shtml

Repeat Analysis

Filtering Out Repetitive Elements - RepeatMasker
http://ccr-081.mit.edu/Repeats.html

Genetic Information Research Institute, including Censor Server
http://www.girinst.org/index.html

Multiple Sequence Alignment

GeneBee
http://www.genebee.msu.su/

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

TreeView
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

ClustalW & ClustalX
http://www.csc.fi/molbio/progs/clustalw/

Restriction Digestion

Webcutter
http://www.firstmarket.com/cutter/cut2.html

Motif Searching

TRANSFAC - The Transcription Factor Database
http://transfac.gbf.de/TRANSFAC/index.html

GENOMATIX - Matinspector, etc.
http://www.genomatix.de/

Pattern Search and Discovery - Institute Pasteur
http://bioweb.pasteur.fr/seqanal/motif/intro-uk.html

THE MEME/MAST SYSTEM - Motif Discovery and Search
http://meme.sdsc.edu/meme/website/

MARS

MarFinder - FutureSoft
http://www.futuresoft.org/MarFinder/

MAR - ChrClass
ftp://ftp.ncbi.nih.gov/pub/kondrashov/MAR/

GENE ONTOLOGY

OntoExpress
http://vortex.cs.wayne.edu/Projects.html

Other Software

GenMAPP - visualize gene expression data on maps representing biological pathways and groupings of genes.
http://www.genmapp.org/

Send comments to: dwomble@genetics.wayne.edu

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