Resources

Useful Links

http://www.brenda-enzymes.org/- Enzyme information database

http://salis.psu.edu/software/ - Salis Lab RBS Calculator

http://www.ecocyc.org/ - Database for E. coli genome, transcriptional regulation, and metabolic pathways

http://www.metacyc.org/- Similar to EcoCyc, but for many other organisms

http://mfold.rit.albany.edu/- UNAFold (combination of mFold and DINAMelt software): RNA folding and DNA hybridization/melting prediction

http://bioinformatics.biol.rug.nl/websoftware/ppp/ppp_start.php - Promoter Prediction Software

http://www.genome.jp/kegg - Kyoto Encyclopedia of Genes and Genomes

http://regulondb.ccg.unam.mx/ - RegulonDB, E. coli Transcriptional Network

http://partsregistry.org/Main_Page - Standard Registry of Biological Parts

http://www.addgene.org/ - Plasmid Database

http://bionumbers.hms.harvard.edu/ - Database of useful biological numbers

http://www.synberc.org/- Synthetic Biology Engineering Research Center

http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=main - Regulation and Transcription Factor Binding Site Database

http://www.biofab.org/data - BIOFAB: International Open Facility Advancing Biotechnology

http:// bioinformatics.bc.edu/clotelab/RNAiFold- RNAiFold: RNA inverse folding problem- find RNA sequence using given target secondary structure

http://genomes.urv.es/OPTIMIZER/ - Codon Optimizer for prokaryotes

http://berry.engin.umich.edu/gene2oligo/ -  Gene2Oligo: oligonucleotide design for in vitro gene synthesis

http://nihserver.mbi.ucla.edu/RACC/ -  Rare codon calculator (RaCC) for E. coli

http://cgsc.biology.yale.edu/AcadCharges.php - The Coli Genetic Stock Center

http://rna.informatik.uni-freiburg.de:8080/IntaRNA/Input.jsp - IntraRNA- RNA-RNA Interaction calculator

http://rna.informatik.uni-freiburg.de:8080/CopraRNA/Input.jsp - CopraRNA- sRNA Targeting

http://regprecise.lbl.gov/RegPrecise/ - Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes

http://molbiol-tools.ca/Repeats_secondary_structure_Tm.htm​ - List of Tools for Identfiying Repeats, Secondary Structure, and Melting Temperature for RNA & DNA