Resources

 

Useful Links

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

https://salislab.net/software/ – Salis Lab RBS and promoter 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://www.unafold.org/ – UNAFold (combination of mFold and DINAMelt software): RNA folding and DNA hybridization/melting prediction

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

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

http://parts.igem.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://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

https://openebench.bsc.es/tool/gene2oligo – Gene2Oligo: oligonucleotide design for in vitro gene synthesis

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

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

https://rna.informatik.uni-freiburg.de/CopraRNA/Input.jsp – CopraRNA – sRNA Targeting

https://regprecise.lbl.gov/ – Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes

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

https://ebrc.org/ – Engineering Biology Research Consortium

https://ebrcintranslation.buzzsprout.com/ – Podcast on various topics in Engineering Biology