Biology Resources

These are resources related to biology that may be useful to chemists doing biology (or, I suppose, biologists doing biology). Feel free to contact me if you find any others that are generally useful; this list will grow.

Databases

• DBTBS - http://dbtbs.hgc.jp/
• from the site's description: "a collection of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of B. subtilis genes"
• partsregistry (Registry of Standard Biological Parts) - http://partsregistry.org/Main_Page
• from the site's description: "a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems"
• PubMed - http://www.ncbi.nlm.nih.gov/pubmed/
• come on guys; please know you've heard of PubMed
• literature searching (PubMed)
• other useful tools through the same portal:
• Nucleotide - http://www.ncbi.nlm.nih.gov/nuccore - collection of DNA sequences from several depositories
• Protein - http://www.ncbi.nlm.nih.gov/protein - collection of sequences from several databses
• BLAST - http://blast.ncbi.nlm.nih.gov/Blast.cgi - sequence similarity searching

Tools

• IDT SciTools - http://www.idtdna.com/scitools/scitools.aspx
• note: IDT is a company that sells oligonucleotides
• the SciTools are freely available; Oligo Analyzer is particularly useful for RNA primer design
• ExPASy - http://us.expasy.org/
• from the site's description: "ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc"
• many useful tools on this portal; see for example PeptideMass (gives expected masses given specific digests of peptides)