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Molecular Databases and Tools
DNA and RNA
The Broad Institute, a collaboration of MIT, Harvard and the Whitehead Institute of Biomedical Research, has released the sequenced genome of a female boxer, Tasha. The project is described in the December 8, 2005 issue of Nature.
A database of Drosophila genes and genomes with various analytical tools including BLAST and GBrowse. Developed by the Biology Department at Indiana University with funding from the National Human Genome Research Institute.
GenBank, National Center for Biotechnology Information
A public archive of DNA and RNA sequences that is searchable by keywords, including organism, gene name, and genome project. Do search through Entrez Nucleotide and look for accession numbers starting with letters other than N. Compare to RefSeq, listed below.
Human Genome Project: Gene Gateway
A portal to guides and tutorials that explain how to use the many tools developed to analyze the huge volume of data about the human genome. The tools explained include: Online Mendelian Inheritance in Man (OMIM), National Center for Biotechnology Information's (NCBI) GenBank, and many more.
International Sequencing Consortium
This site provides a database of all genome projects in progress throughout the world. Find out which groups are sequencing which organisms and who is funding the research.
RefSeq, National Center for Biotechnology Information
A collection of curated DNA, RNA and protein sequences that is searchable by keywords, including organism, gene name and genome project. The best sequence for each gene from an organism is chosen from GenBank, confirmed, and references from further work are added. Do search through Entrez Nucleotide and look for accession numbers containing an underscore.
Rhesus Macaque Genome Resources
The rhesus macaque genome sequence was published in April 2007. Use these tools at the National Center for Biotechnology Information (NCBI) to explore the primate genome.
Proteins
BLAST (Basic Local Alignment Search Tool) National Center for Biotechnology Information
Use Protein Blast to search your protein sequence against known proteins. The statistical significance of matches are calculated for you.
CCD (Conserved Domains Database), National Center for Biotechnology Information
Enter your protein sequence to see if it matches conserved domains from known proteins.
MMDB (Molecular Modeling Database) National Center for Biotechnology Information
Use MMDB to match your protein sequence against 3-dimensional protein models from the Protein Data Bank, and then view the structure in Cn3D 4.1, a downloadable helper application.
Protein Clusters Database, National Center for Biotechnology Information
"This collection of related protein sequences (clusters) consists of Reference Sequence proteins encoded by complete genomes . . . . The Protein Clusters database provides easy access to annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods."
"The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase, the UniProt Reference Clusters, and the UniProt Archive. The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data."
