Main Menu
In-state Resources
| SWBIC - Southwest Biotechnology and Informatics Center | http://www.swbic.org/products/bioinfo/bioinfo.php |
Out-of-state Resources
| Metabolic Pathways | |
|---|---|
| Expasy Pathways | www.expasy.org/cgi-bin/search-biochem-index |
| Roche Applied Science where you can access their Biochemical Pathways wall chart | www.roche-applied-science.com/frames/frame_metamap.htm |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) Metabolic Pathways | www.genome.jp/kegg/ligand.html |
| E.Coli Pathways at ECOCYC | biocyc.org/ECOLI/class-subs-instances?object=Pathways |
| PathDB | www.ncgr.org/pathdb/ |
| REACTOME | www.reactome.org |
| EMP - Enzymes and Metabolic Pathways | www.empproject.com |
| PUMA2 Evolutionary Analysis of Metabolism | compbio.mcs.anl.gov/puma2/cgi-bin/index.cgi |
| University of Minnesota Biocatalysis/Biodegradatation Database (UM-BBD) | umbbd.ahc.umn.edu |
| SoyBase - Soybean Metabolism | soybase.ncgr.org/cgi-bin/ace/generic/search/soybase |
| Metalgen - Genes and Metabolism | chlora.lgi.infobiogen.fr:1234/Indigo |
| Metabolic Pathways of Biochemistry, the online reference of metabolism for students, scientists, and the world. This site is designed to graphically represent all major metabolic pathways, primarily those important to human biochemistry. | www.gwu.edu/~mpb/ |
| International Union of Biochemistry & Molecular Biology (IUBMB)-Nicholson Minimaps | www.tcd.ie/Biochemistry/IUBMB-Nicholson/ |
| Regulatory Pathways | |
|---|---|
| KEGG Regulatory Pathways | www.biologie.uni-hamburg.de/b-online/kegg/kegg/Classes/regulation.html |
| The Signaling PAthway Database (SPAD) | www.grt.kyushu-u.ac.jp/spad1 |
| CSNDB - Cell Signaling Networks | geo.nihs.go.jp/csndb |
| Comprehensive Yeast Genome Database (CYGD)- Yeast Pathways at Munich Information Center for Protein Sequences (MIPS) | mips.gsf.de/proj/yeast/CYGD/db/pathway_index.html |
| TRANSPATH - Gene Regulatory Pathways | transpath.gbf.de |
| GenMapp | www.genmapp.org/default.as |
| Wnt Signaling Pathway | www.stanford.edu/~rnusse/wntwindow.html |
| HOX-Pro - Homeobox Genes Database | www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html |
| GeNet - Gene Networks Database | www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm |
| Interactive Fly - Drosophila Genes | flybase.bio.indiana.edu/allied-data/lk/interactive-fly/aimain/1aahome.htm |
| FlyNets - Drosophila Molecular Interactions | gifts.univ-mrs.fr/GIFTS_home_page.html |
| GIF_DB - Drosophila Gene Interactions | gifts.univ-mrs.fr/GIFTS_home_page.html |
| Protein-Protein Interactions | |
|---|---|
| PathDB | www.ncgr.org/pathways |
| Database of Interacting Proteins (DIP) | dip.doe-mbi.ucla.edu |
| Biomolecular Interaction Network Database (BIND) | bind.ca |
| BRITE: Biomolecular Relations in Information Transmission and Expression | www.genome.jp/brite |
| Transcription Factors | |
|---|---|
| TRANSFAC - Transcription Factor Database | www.gene-regulation.com/pub/databases.html#transfac |
| RegulonDB - E. coli Transcriptional Regulation | www.cifn.unam.mx/Computational_Genomics/regulondb |
| DBTBS - B. subtilis Transcription Factors | dbtbs.hgc.jp |
| DPInteract - Database on DNA-protein interactions | arep.med.harvard.edu/dpinteract |
| Sequence Analysis | |
|---|---|
| NCBI BLAST | www.ncbi.nih.gov/BLAST/ |
| X Genome Initiative Software (XGI) | www.ncgr.org/xgi |
| Clustal W | www.ebi.ac.uk/clustalw/ |
| BLASTZ (Sequence Alignment Tool) | www.psc.edu/general/software/packages/blastz |
| CINEMA (Sequence Editing Tool) is a Colour INteractive Editor for Multiple Alignments that provides visualization and editing of multiple alignments of either protein or DNA sequences | www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2.02 |
| SAM (Sequence Alignment and Modeling system) | www.cse.ucsc.edu/research/compbio/sam.html |
| RepeatMasker (Repeat Masking) | www.repeatmasker.org |
| VISTA is a suite of web-enabled alignment and visualization tools along with a sequence data base consisting of pre-computed whole genome alignments | www-gsd.lbl.gov/vista/index.shtml |
| mVISTA Standalone version of VISTA | www-gsd.lbl.gov/vista/mvista/submit.shtml |
| Motif/Protein Families | |
|---|---|
| InterPro | www.ebi.ac.uk/interpro/ |
| BLOCKS | blocks.fhcrc.org/ |
| THE MEME/MAST SYSTEM -(Motif and Pattern Matching Tool) | meme.sdsc.edu/meme/website |
| Genes | |
|---|---|
| GENSCAN | genes.mit.edu/GENSCAN.html |
| GeneSeqer (Spliced Alignment) | bioinformatics.iastate.edu/cgi-bin/gs.cgi |
| Signal Peptides | |
|---|---|
| Signal P | www.cbs.dtu.dk/services/SignalP-2.0 |
| Compounds/Molecules | |
|---|---|
| Klotho: Biochemical Compounds Declarative Database | www.biocheminfo.org/klotho/ |
| KEGG: Kyoto Encyclopedia of Genes and Genome Database - Compound Search | www.genome.jp/kegg/ligand.html |
| ChemFinder | www.chemfinder.com |
| International Union of Pure and Applied Chemistry | www.chem.qmw.ac.uk/iupac |
| ChemWeb | www.chemweb.com |
| Cheminformatics/Chemoinformatics glossary at the Cambridge Healthtech Institute | www.genomicglossaries.com/content/chemoinformatics_gloss.asp |
| Sequence Databases | |
|---|---|
| GenBank | www.ncbi.nlm.nih.gov/GenBank |
| European Molecular Biology Laboratory (EMBL) | www.ebi.ac.uk |
| DNA Data Base of Japan (DDBJ) | www.ddbj.nig.ac.jp |
| Proteins | |
|---|---|
| Swiss-Prot | us.expasy.org/sprot |
| Uni-Prot- The Universal Protein Resource | www.expasy.uniprot.org/index.shtml |
| ExPASy (Expert Protein Analysis System) proteomics server | au.expasy.org |
| Protein Information Resource (PIR) | pir.georgetown.edu |
| Protein Data Bank (PDB) | www.rcsb.org/pdb |
| Cambridge Crystallographic Data Centre | www.ccdc.cam.ac.uk |
| Molecular Visualization Freeware Protein Explorer, Chime & RasMol | www.umass.edu/microbio/rasmol |
| Citation Databases | |
|---|---|
| Highwire Press | highwire.stanford.edu |
| PubMed | www.ncbi.nlm.nih.gov/entrez |
| SiteSeer- Scientific Literature Digital Library | citeseer.ist.psu.edu/cs |
| Scirius | www.scirus.com |
| Biomednet | www.bmn.com |
| ScienceDirect | www.sciencedirect.com (Elsevier) |
| IDEAL | www.idealibrary.com |
| Nature Publishing Group | www.nature.com/nature |
| Wiley InterScience | www.interscience.wiley.com |
| Literature Digests and Locus Specific Databases | |
|---|---|
| On-line Medndelian Inheritance of Man (OMIM) | www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM |
| GeneReviews | www.geneclinics.org |
| Taxonomy | |
|---|---|
| NCBI Taxonomy | www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html |
| GRIN | www.ars-grin.gov |
| Multiple Source Searching | |
|---|---|
| NCBI ENTREZ | www.ncbi.nlm.nih.gov/Entrez/ |
| Gene Expression | |
|---|---|
| GeneX-Lite | www.ncgr.org/genex |
| NCBI Gene Expression Omnibus | www.ncbi.nlm.nih.gov/geo |
| NCBI UniGene Database | www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene |
| Affymetrix Gene Chip analysi | www.affymetrix.com/analysis/index.affx |
| MIAME standards | www.mged.org/Workgroups/MIAME/miame.html |
| MAGE | www.mged.org/Workgroups/MAGE/mage.html |
| Ontologies | |
|---|---|
| Gene Ontology Consortium (GO) | www.geneontology.org |
| Nomenclature | |
|---|---|
| IUBMB Nomenclature | www.iubmb.unibe.ch |
| IUPAC Nomenclature | www.chem.qmul.ac.uk/iupac |
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