posted: November 16, 2021
pythonsequencingDNAbeginner
Two strands of DNA bound together? Simple right? Well turns out there's more to it especially with the funny 5' 3' prime business. Learn how to convert between the two strands in python.
It is standard practice that unless otherwise stated, a nucleotide sequence is written left to right beginning with its 5’ (five-prime) phosphate end and then ending with its 3’ (three-prime) hydroxyl end where 5’ and 3’ refer to the position of these groups on the 5-sided sugar ring (ribose or deoxyribose) of the backbone. When working with single stranded oligonucleotides that’s the end of the story, but often double stranded DNA or RNA species are utilized. In those cases, there are two diffe...
posted: November 13, 2021
buffers
A list of commonly used solutions in the lab along with guidelines how to prepare them.
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posted: November 08, 2021
aminoacidsproteins
A table of useful properties for the common 20 amino acids.
download the table here: amino_acid_table.csv...
posted: November 07, 2021
chemistrymassspectrometry
A tool to look up compounds by name in Pubchem and get their chemical formula and exact mass plus or minus a proton. Useful for small molecule mass spectrometry.
the tool: exact mass tool...
posted: November 07, 2021
translationcodons
A collection of CSV files that contain codon to amino acid translation and relative frequency information across organisms: ecoli, human
I've provided the codon usage files here as both downloadable links and tables on the page. If you would like a particular organism to be added please contact me. ...
posted: November 07, 2021
uniprotproteinsrestapipython
UniProt is a great online resource for finding a wealth of information about proteins from nearly all model organisms. Searching it manually works well, but to get to the next level of protein data mining you'll likely need to access its data programmatically, via the hidden REST API.
The Universal Protein Resource more commonly referred to as just UniProt is an online resource that contains protein sequences and associated data from more than a dozen different organisms including humans. This curated database aims to be a universal resource that ties together disparate data from a wide variety of sources into a single, central location. This data includes structural information, isoform data, subcellular localization, reported variants and associated pathologies, and much mo...
