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HOME | SERVICES | TOOLS | WORKSHOPS | RESOURCES | PEOPLE |
| This is not meant to be a complete list of all available resources. Rather, it is a list of resources that we have found useful. If you know of a resource that you find useful that is not on the list, please email the bioinformatics core and we will add it to the list. |
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Databases |
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| DNA | Note: GenBank and EMBL mirror data but each has its own strengths in terms of interfaces and tools. |
| GenBank | The central repository in the United States for sequence based data. Many databases and tools are available here. |
| EMBL | European Molecular Biology Laboratory sequence repository. |
| Protein | |
| Swiss-Prot | Many tools and resources for protein analyses. |
| PIR | Protein Information Resource. |
| PROSITE | A database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. |
| InterPro | A useful resource for whole genome analysis and has already been used for the proteome analysis of a number of completely sequenced organisms including preliminary analyses of the mouse and human genomes. |
| PDB | Repository for the processing and distribution of 3-D biological macromolecular structure data |
| Genomic | |
| ENSEMBL | Nice graphical displays of genomic assemblies (human, mouse and others) |
| UCSC | Displays annotation on the assembled human and mouse genomes. Nice sequence based query tool and display. |
| The Human Genome Database | International collaboration in support of the Human Genome Project |
| Human genome at NCBI | GenBank view of the Human genome. |
| UCSC HGP Working Draft | Public human and mouse genomic assemblies. Nice sequence based query tool with good visualization. |
| MGD at JAX | Mouse genome database at Jackson Labs. |
| FlyBase | Database for Drosophila genome and annotation |
| SGD | Saccharomyces genome database |
| PlasmoDB | Database for the Plasmodium genomic sequence. Developed here at Penn jointly by the laboratories of David Roos and Chris Stoeckert. |
| WormBase | Genomic sequence and annotation for C. elegans. |
| Gene Indices | |
| AllGenes | Integrates genomic and protein sequences for human and mouse around assembled transcripts. Powerful query interface. Developed here at Penn in CBIL. |
| TIGR Gene Indices | Similar to AllGenes. Includes many different organisms. |
| Other Databases | |
| GeneCards | Integrated database containing information from a variety of sources. Organized around official gene names. |
| Source | Useful for obtaining information about sequences given accessions or image clone identifiers. |
Tools |
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| EBI Toolbox | Tools for database and homology searching, browsing and analysis including FASTA, CLUSTALW, MSA, PSA |
| BCM Search Launcher | Tools for secondary structure prediction, multiple sequence alignment, gene finding, etc. |
| TIGR software | Tools for splice sites detection, gene finding, genomic sequence alignment, sequence assembly, expression data visualization and analysis. |
| GenScan | Provides access to the program Genscan for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms |
| MOTIF | Tools to search protein and nucleic acid sequence Motifs |
| PatScan | Searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input |
| SCOP | Tools for structural classification of proteins |
Pathways |
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| KEGG | Kyoto Encyclopedia of Genes and Genomes (KEGG) is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways. |
| BioCarta | Provides interactive graphic models of molecular and cellular pathways |
| MetaCyc | Contains metabolic pathways from 150 different organisms |
Microarray |
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| Databases | |
| NCI ArrayDB | A Gene Expression Database for the Molecular Pharmacology of Cancer |
| EBI ArrayExpress | A public repository for well annotated microarray based gene expression data |
| ExpressDB | Harvard's relational database containing yeast and E. coli RNA expression data |
| Stanford Microarray Database | Raw and normalized data from microarray experiments with the corresponding image files. Data is released to the public at the researcher's discretion or upon publication. |
| ChipDB | MIT's interactive database of expression data |
| Data Analysis Tools | |
| EBI Expression Profiler | A set of tools for clustering, analysis and visualization of gene expression and other genomic data |
| Sanger Center ExpressionBrowser | A tool for visualizing clusters of expression data |
| J-Express | A Java implementation of hierachical clustering, self organized maps, and principal component analysis, with several different viewing options and output formats. |
| Cluster/TreeView | Cluster and TreeView are an integrated pair of programs for analyzing and visualizing the results of complex microarray experiments. |
| 2HAPI | A web-based microarray data analysis system to browse, visualize, and analyze data obtained from genome-wide gene expression experiments. |
Statistics |
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| StatSoft Electronic Statistics Textbook | A searchable electronic textbook for general statistical concepts |
Software |
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| BioPerl | Open source Perl tools for bioinformatics, genomics and life science research. |
| EMBOSS | A package of free open source software for sequence analysis provided by the EMBL. |
