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—Databases  
 
—Tools
Bioreagents
Database of curated commercially available antibodies AbMiner: antibody database        
Database of antibodies available for purchase AbCAM: antibody search engine        
Database of primers for real-time PCR RTPrimerDB: Primers for real-time PCR        
Genomes 
Go to BioFAQ on SGD SGD: Saccharomyces Genome Database      
Candida Genome Database CGD: Candida Genome Database      
Flybase genome database Flybase        
Rat genome database RGD: Rat genome database        
Arabidopsis genome database TAIR: Arabidopsis genome database        
Tetrahymena Genome Database TGD: Tetrahymena genome database      
Zebrafish Genome Database ZFIN: Danio rerio (Zebra fish) genome database        
Genes, proteins & sequence analysis
Database of curated protein interactions data BIND: protein interactions   Resource requires a login - click here to get one    
European Molecular Biology Open Software Suite, basically open source GCG EMBOSS: molbio tools        
Database of curated protein interactions data DIP: protein interactions        
Database of homologs among the annotated genes of completely sequenced eukaryotic genomes HomoloGene: protein homologs        
Database of homologous vertebrate genes HOVERGEN: protein homologs        
GO Ontologies GO ontologies      
Database of curated sequences, mutation and ligand binding data for GPCRs GPCRDB        
Collection of integrated databases pertaining to immune proteins from vertebrates ImMunoGeneTics database        
iHOP NLP extraction of gene function from literature iHOP gene properties        
Database of curated sequences, mutation and ligand binding data for nuclear receptors NucleaRDB        
Classification of proteins into functionally related subfamilies PANTHER protein classification & expression analysis        
Tool for drawing pathways and other types of biological objects PathwayBuilder illustrator Stanford only This resource is restricted to holders of a SUNet ID; click here to see how to get one    
Premiere diagraming tool for MS Office MS Visio diagramming tool Stanford only Resource requires a login - click here to get one    
gene-to-GO term associations PubGene: Graphical Go/PubMed gene associations        
Expression & function
DNA binding site prediction using microarray data BioProspector: DNA motif prediction      
DNA binding site prediction using microarray and comparative genomics data CompareProspector: DNA motif prediction      
Comprehensive database of curated microRNA sequence data, annotation and predicted gene targets miRbase: miRNA data        
Database of curated microRNA and microRNA target gene data miRNAMap: miRNA data        
Database of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa MitoRes: nuclear-encoded mitochondrial gene products        
Database of protein and peptide identifications PRIDE: protein and peptide identification data        
Database of UTR sequences UTRdb: untranslated transcript sequences        
transcript start site data based on SAGE 5'SAGE: transcript start sites        
Powerful method for evaluating the significance of microarray gene expression measurements SAM: Significance Analysis of Microarrays   Resource requires a license agreement - click here to get one  
Literature & biodata mining
Literature searching way beyond PubMed Web of Science: ultimate literature searching Stanford only      
Highly comprehensive database of biological literature BIOSIS, for broader coverage of the biological literature than PubMed Stanford only      
Metatool for identifying candidate transcription factor binding motifs in DNA sequences BEST : DNA binding motif identification        
Tool for interpreting lists of genes identified through microarray experiments using GO GoMiner gene expression analysis        
Powerful tool for phylogenetic analysis MEGA phylogenetic analysis        
Program for identifying conserved motifs in DNA and protein sequences MEME motif identification        
Program for searching DNA and protein sequences using motifs MAST database motif searching        
Facilitates access to data commonly sought after for clones, GenBank accession numbers, genes, etc SOURCE      
Structures 
ChimePro is the molecular structure viewer provided by MDL Chime Pro viewer        
RasMol is a classic molecular structure viewer RasMol viewer        

Bioresearch Notifications

Solution biotool: Ingenuity Pathways Analysis

Need to analyze microarray or proteomics data? If so, have look at the Ingenuity Pathways Analysis (IPA), a highly curated database + analytical functions for understanding how proteins work together to effect cellular changes. More
Already an IPA user? Then join the online Stanford IPA user group and share in your colleagues' expertise.

So What? Success Tip #11



Need to get up to speed with an unfamiliar concept in bioinformatics, genomics, genetics or proteomics? Try EBGGBP - you won't be disappointed!

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PharmGKB is a major repository of pharmacogenomic data for Homo sapiens. Its principal investigator is Stanford Professor of Bioengineering Russ B. Altman. The GO Ontologies are the principal ontologies describing the properties of genes and proteins of many organisms. One of its architects is Stanford Genetics Professor J. Michael Cherry. SMD is a major repository of microarray gene expression. The database is a joint project in the Departments of Biochemistry and Genetics at the School of Medicine, Stanford University. SOURCE is a data retrieval tool provided by the Department of Genetics at the School of Medicine, Stanford University.
[more] SGD is the main repository of genome data from Saccharomyces cerevisiae. Its principal investigator is Stanford Genetics Professor J. Michael Cherry.
[more] TGD is the main repository of genome data from Tetrahymena thermophila. Its principal investigator is Stanford Genetics Professor J. Michael Cherry. TGD is the main repository of genome data from Candida albicans. Its principal investigator is Stanford Genetics Assistant Professor Gavin Sherlock. SAM is a powerful tool for evaluating the statistical significance microarray gene expression data. The tool is provided by Stanford Professor of Statistics Robert Tibshirani. TGD is the main repository of genome data from Tetrahymena thermophila. Its principal investigator is Stanford Genetics Professor J. Michael Cherry. TAIR is the main repository of genome data from Arabidopsis thaliana. It is curated by personnel form Stanford's Department of Plant Biology. Using microarray data, BioProspector examines the upstream region of genes in the same gene expression pattern group, looking for regulatory sequence motifs. It was developed by Stanford Biochemistry Professor Douglas L. Brutlag. A powerful tool for microarray and genome data analysis, BioProspector examines the upstream region of genes in the same gene expression pattern group, looking for regulatory sequence motifs. It was developed by a team that includes a number of Stanford researchers. Using combined tiling array and comparative genomics data, CisGenome was developed by a team that includes Stanford Professor of Statistics Wing Wong. This resource is restriced to holders of a SUNet ID. StepMiner was developed by a team that includes Stanford Professor of Statistics Robert Tibshirani, Stanford Associate Professor of Radiology Sylvia K. Plevritis, and Stanford Professor of Computer Science David L. Dill.
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