Baneyx BioNano Laboratories.

Genomics Resources
All things E. coli including aggregated searches on 12 different data sources
Community contributed content on E. coli
A good site for rapid look-up of E. coli genes
Excellent site for complete, up-to-date information on E. coli genes. Includes links to PDB, SWISS-PROT and ASKA/KEIO deletion collections
Japanese genome analysis project on E. coli W3110. Includes ASKA/KEIO collections, microarray, 2D proteome and expression data.
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
Bioinformatics database describing the genome, regulatory and biochemical machinery of E. coli
Pathway and gemome databases for many organisms
Information on all the publicly available, complete prokaryotic genomes
E. coli genome and proteome database
Database of E. coli regulons and transcriptional regulatory elements
Promoters and Terminators Software for promoter/terminator predictions
Common genotypes A simple description of common genetic markers and mutations from NEB
List of essential E. coli genes from the Blattner's lab as of March 2004
Codon usage frequencies in ≈ 36,000 organisms
Proteomics Resources
Protein sequence database at ExPASy
Protein sequence database at Entrez
Protein structure database at Entrez
Protein structure database at RCSB-PDB
Automated protein homology modeling at ExPASy
Clickable 2D-PAGE gels including E. coli at ExPASy
N-terminal protein sequence from 2D-gels of E. coli grown under a variety of conditions at the Church laboratory
Links protein mutations to articles that describe them
Ecce The E. coli cell envelope protein data collection: functional classification of inner membrane, periplasmic and outer membrane proteins in E. coli.
TMB-Web Web resources on transmembrane barrel proteins
MP 3D structure An up to date repository of known crystal structures for membrane proteins
MEROPS Protease database
Collection of single gene knock out mutants
Archive clones containing all predicted E. coli ORFs as His-tagged proteins with or without a C-terminus GFP fusion
Searchable Kohara collection
Strains and mutants from the CGSC at Yale
Strains and mutants from the American Type Culture Collection
Strains and plasmids from the Shigen laboratory collection
Strains and plasmids from the Belgian Coordinated Collection of Microorganisms
Interactive periodic table with extensive information on chemical elements and their compounds
Crystal structure
An excellent primer on crystalline materials structures
Online version of the CRC handbook of chemistry and physics. A treasure trove of information
Multiple sequence alignments for DNA and proteins at EMBL
Sequence similarity searches for DNA and proteins at EMBL
Genomewide similarity searches at EMBL
Many useful proteomics tools at ExPASy including protein parameters (pI, MW, aa information...), post-translational modifications...
SCRATCH Protein Predictor Predicts many protein properties (from solvent accessibility to solubility upon overexpression and antigenicity) from primary structure information
AGGRESCAN Predicts aggregation "hotspots" in proteins
Peptide Property Calculator A GenScript resource that predicts peptide properties and best solvent from amino acid sequence
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
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
Interactive buffer recipes from EMBL Heidelberg
Calculates molecular weights and provide other information on querried compounds
Web interface from DKFZ Heidelberg that creates animated GIF from PDB files
Article search
Full access to online journals - UW restricted
Citation/keyword searchable database including abstracts from journals not indexed in PubMed - UW restricted
Technical information on enzymes including assays
Information on fluorescence probes and techniques
User Facilities & Centers
University of Washington Nanotech User Facility
Mass spectrometry service center at the School of Pharmacy
University of Washington Center for Nanotechnology
University of Washington MRSEC
National Nanotechnology Infrastructure Network
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Contact: François Baneyx, University of Washington, Department of Chemical Engineering, Box 351750, Seattle, WA Tel: 206-685-7659 Fax: 206-685-3451 E-mail:

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