Genetics and Bioinformatics Databases and Tools

National Center for Biotechnology Information Home of Entrez, THE American gateway to all the major databases of DNA, RNA, and protein sequences, genomes, Mendelian Genetics info (OMIM), STSs, SNPs, etc., etc., etc... Also houses bioinformatics tools such as BLAST (Basic Local Alignment Sequence Tool), so you can work with the data you retrieve. Unbelievably vast and interlinked, including to literature databases such as PubMed. Be sure to check out the "Bookshelf" of biomedical books which can be accessed FREE online. For those of you budding Biochemists, it even includes Stryer's Biochemistry text! Also take a look at "Coffee Break" with fun, short science articles, and "Genes and Diseases". European Molecular Biology Laboratory The - older - European version of the NCBI. Home of the EBI (European Bioinformatics Institute) at http://www.ebi.ac.uk. Good place to start looking for European science policy. The EBI site also includes FlyBase with ImageBrowse, so you can see what mutations look like. Synthetic Biology (iGEM Registry of Standard Parts) Catalog of interchangeable biological components that can be used to build biological systems and devices. Used in iGEM (International Genetically Engineered Machine) Competitions. NEB WebCutter 2.0 A restriction mapping and genetic engineering tool. Allows virtual restriction digestion (cutting) of DNA with hundreds of enzymes. You can either import and cut your own sequence, or you can cut the DNAs pre-loaded in the drop-down menus. FunDO FunDO stands for FUNctional Disease Ontology Annotation. It allows you to input a list of genes (like a bunch of genes you may have identified as having been upregulated during a DNA microarray experiment) and comes up with a diagram of diseases to match the gene expression pattern. Includes a tutorial and a sample list of genes to try. ApE: A Plasmid Editor Freely downloadable DNA restriction map drawing software. The Human Protein Atlas An atlas of pretty microsopic images that show where a particular (antibody-stained) protein ends up in a cell or a tissue. To use the database, simply input a gene symbol or protein name to find protein expression profiles for a large number of human tissues, cancers and cell lines, subcellular protein localization in three cell lines, and RNA transcript expression levels in three cell lines. You can also use Fields in the Search function to find all proteins expressed in a certain organ or specific tissue, located in a certain subcellular compartment or differentially expressed in a given tumor type. Having a BLAST (and avoiding BLASTphemy) A good review on BLAST, how it works, and what the pitfalls are. The Wodak Lab: Bioinformatics and Computational Biology Tools A whole bunch of computational tools to help researchers investigate protein interactions with other proteins, DNA and other molecules. VecScreen Allows you to BLAST your DNA sequence to make sure it really is what you think it is, and not just a lost piece of cloning vector. Cis Regulatory Elements in Mammalian Genome Search Tool Put in a bunch of gene sequences you know are co-expressed, and the program will help identify conserved transcription factor binding sites (the idea being that co-expressed genes are probably co-regulated by a common transcription factor). BacMap Genome atlas and interactive maps of over 1600 fully sequenced bacterial genomes. University of Colorado Bioinformatics Tutorials and Problem Sets Pathbase (Mouse Phenotyping by Histopathology) Mutant mouse pathology database (microscopic and macroscopic images searchable by lesion of genetic locus).