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Genomics Resources
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A good site for rapid look-up of E. coli genes |
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Excellent site for complete, up-to-date information on E. coli genes. Includes links to PDB, SWISS-PROT and ASKA/KEIO deletion collections |
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Japanese genome analysis project on E. coli W3110. Includes ASKA/KEIO collections, microarray, 2D proteome and expression data. |
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Homepage of the Blattner's lab. Includes clone collection in Gateway vectors, single gene deletion collection, microarray data, phenotypic analysis data, BLAST and annotation tools |
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Bioinformatics database describing the genome, regulatory and biochemical machinery of E. coli |
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Pathway and gemome databases for many organisms |
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Information on all the publicly available, complete prokaryotic genomes |
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E. coli genome and proteome database |
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Database of E. coli regulons and transcriptional regulatory elements |
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List of essential E. coli genes from the Blattner's lab as of March 2004 |
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Codon usage frequencies in ≈ 36,000 organisms |
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Proteomics Resources
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Protein sequence database at ExPASy |
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Protein sequence database at Entrez |
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Protein structure database at Entrez |
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Protein structure database at RCSB-PDB |
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Automated protein homology modeling at ExPASy |
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Clickable 2D-PAGE gels including E. coli at ExPASy |
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N-terminal protein sequence from 2D-gels of E. coli grown under a variety of conditions at the Church laboratory |
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Links protein mutations to articles that describe them |
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Collections
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Collection of single gene knock out mutants |
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Archive clones containing all predicted E. coli ORFs as His-tagged proteins with or without a C-terminus GFP fusion |
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Searchable Kohara collection |
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Strains and mutants from the CGSC at Yale |
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Strains and mutants from the American Type Culture Collection |
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Strains and plasmids from the Shigen laboratory collection |
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Strains and plasmids from the Belgian Coordinated Collection of Microorganisms |
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Nanofabrication
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Interactive periodic table with extensive information on chemical elements and their compounds
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Online version of the CRC handbook of chemistry and physics. A treaure trove of information
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Tools
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Multiple sequence alignments for DNA and proteins at EMBL |
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Sequence similarity searches for DNA and proteins at EMBL |
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Genomewide similarity searches at EMBL |
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Many useful proteomics tools at ExPASy including protein parameters (pI, MW, aa information...), post-translational modifications... |
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Conversion tools and calculators for molecular ratio of insert to vector in ligations and oligonucleotides melting temperatures from Promega |
| Oligo Analyzer |
Primer design client. Includes melting temperature, homo and heterodimers, and hairpin predictions |
| Primer X |
Automated design of mutagenic primers for site-directed mutagenesis |
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Predicts PCR products and amplification efficiency of genomic DNA based on user-defined primers |
| NEBcutter |
Identifies unique restriction sites for Type II and commercially available Type III restriction enzymes on DNA sequences as large as 300 kbp |
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Interactive buffer recipes from EMBL Heidelberg |
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Calculates molecular weights and provide other information on querried compounds |
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Web interface from DKFZ Heidelberg that creates animated GIF from PDB files |
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Others
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Literature
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Article search |
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Full access to online journals - UW restricted |
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Citation/keyword searchable database including abstracts from journals not indexed in PubMed - UW restricted |
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Technical information on enzymes including assays |
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Information on fluorescence probes and techniques |
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User Facilities & Centers
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University of Washington Nanotech User Facility |
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Mass spectrometry service center at the School of Pharmacy |
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University of Washington Center for Nanotechnology |
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University of Washington MRSEC |
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National Nanotechnology Infrastructure Network |
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