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Useful
Links
Genome
Sequences
- Genomes OnLine Database
(GOLD) tracks
the progress of genome sequencing efforts
- MicrobesOnline
provides comparative genomics tools to analyze prokaryotic genomes
Mass
Spectrometry / Protein Identification
Molecular
Biology Protocols and Techniques
- Current Protocols
(©John Wiley & Sons, Inc.) are available by site license through
UGA Library. Full text is available when accessed from UGA IP address
- The Encyclopedia
of Genetics, Genomics, Proteomics and Bioinformatics focuses on
studies based on the human and mouse genomes, with additional coverage
of other important model eukaryotes and pathogenic bacteria as well.
It is available by site license through UGA Library.
- The Qiagen
BenchGuide (pdf file) contains many protocols and useful tips for
standard molecular biology techniques dealing with plasmid DNA, genomic
DNA, RNA, and protein
- Recombinant
Protein Solubility Prediction. This statistical model predicts protein
solubility assuming the protein is being overexpressed in Escherichia
coli
- Need help troubleshooting
your electrophoresis gels?
Pyrococcus
furiosus Genome Sequences
- The Institute for Genomic
Research (TIGR) Comprehensive Microbial Resource (CMR) [here]
- Integrated Microbial Genomes
(IMG) at the DoE Joint Genome Institute (JGI) [here]
- REFSEQ (through NCBI) [here]
- GenBank (through NCBI) [here]
Sequence
Analysis
- Check the codon usage in
any prokaryotic genome at the Microbial
Genome Codon Usage Database
- The Sequence
Manipulation Suite is a collection of web-based programs for analyzing
and formatting DNA and protein sequences.
- The Oligonucleotide
Properties Calculator will calculate physical constants such as
length, GC content, molecular weight, melting temperature, for an input
sequence of double-stranded or single-stranded DNA or RNA.
- The Peptide
Property Calculator will calculate physical constants such as length,
molecular weight, extinction coefficient, for an input protein sequence.
It will also plot hydropathy and convert a one-letter amino acid code
to three-letter code.
- The Protein
Calculator will calculate physical constants such as molecular weight,
charge at various pHs, UV absorption, numbers of atoms or residues for
an input protein sequence. It will also scan a mass spectrum result
for protein molecular weight.
- The Universal
Protein Resource provides a metasite for access to Swiss-Prot, TrEMBL,
and PIR
- IDT SciTools
from Integrated DNA Technologies is a suite of online programs for DNA
and RNA design, analysis and calculations: comprehensive oligonucleotide
analysis (Oligo Analyzer), primer and probe selection tool (PrimerQuest),
microarray and batch RNAi design (WorkBench), DNA directed RNA interference
(ddRNAi Design), design duplexed RNA oligos for RNA interference (RNAi
Design), antisense oligo design and selection tool (Anitsense Design),
secondary structure prediction tool (mFold), calculation tool for oligo
dilutions (DilutionCalc) and resuspensions (ResuspensionCalc).
- The PSIPRED secondary
structure prediction tool makes highly accurate predictions of secondary
structure, given a protein sequence. Also
available is GenTHREADER, a protein fold recognition tool that can
be applied to individual protein sequences or even an entire proteome.
- PredictProtein is a multifaceted
web service that, given a sequence or alignment, will return multiple
sequence alignments, PROSITE sequence motifs, low-complexity regions
(SEG), nuclear localization signals, regions lacking regular structure
(NORS) and predictions of secondary structure, solvent accessibility,
globular regions, transmembrane helices, coiled-coil regions, structural
switch regions, disulfide-bonds, sub-cellular localization, and functional
annotations.
- ExPASy provides
links to an array of secondary structure prediction tools. This site
contains many other tools for primary structure analysis, topology
prediction, post-translational modification prediction, pattern/profile/motif
searching, and sequence alignment.
- MEME/MAST
allows you to discover motifs in groups of related DNA or protein sequences
and search sequence databases using motifs
- The TMpred
program makes a sequence-based prediction of protein membrane-spanning
regions and their orientation
- STRING (Search Tool for the Retrieval of Interacting Proteins) quantitatively integrates interaction data from genomic context, high-throughput experiments, coexpression data and from available literature
- AlignAce is a tool for finding DNA binding motifs
Shewanella
- A summary
of Shewanella oneidensis, strain MR-1, integrates our evolving
understanding of the genes, proteins, metabolic network, and genetic
network of this important DOE microorganism.
Synchrotron
Radiation/X-ray Properties
- The X-ray
Periodic Table provides edge energies, emission energies, x-ray
cross sections, and fluorescence yields for any element.
Transcription Factors / Promoters
- ArchaeaTF is a database of putative transcription factors from all completed archaeal genomes.
- ExtraTrain covers extragenic regions (up- and downstream of genes) of 230+ genomes corresponding to archaea and bacteria, and information about 26000+ regulators belonging to 16+ families. ExtraTrain also provides a tool to search the information about regulators and includes references associated with regulator entries.
- DOOR (Database of Prokaryotic Operons) is an operon database developed by the Computational Systems Biology Lab (CSBL) at the University of Georgia. The operons in the database are based on prediction.
scott@chem.uga.edu
Department of Chemistry
University of Georgia
Athens, GA 30602-2556
706 542-2240 | FAX: 706
542-2295 |
