posted: June 07, 2022
dataanalysispythonplotlyGoogleColabpandasregex
Learn how to use python in an interactive online Google colab notebook to generate volcano plots to analyze your data sets.
In their most basic form, experiments will generally involve comparing two conditions: a control condition vs an experimental condition where a treatment or perturbation has been applied to the system of interest. The effect of this treatment can then be read out in numerous different ways depending on what you’re interested in understanding about your system. Sometimes this can be accomplished by looking at a small number of factors such as the expression changes in a single protein or changes ...
posted: January 20, 2022
pythondnasequencesrecursion
Learn how the powerful technique of recursion can simply and elegantly generate all possible sequences of a desired length.
Modern DNA synthesis techniques allow for the construction of vast libraries of different DNA sequences that can be used in many high throughput applications. As an example, say you just found that a particular transcription factor binds to a promoter with a defined sequence that is 8 nucleotides long. The natural binding affinity of the factor for the sequence is good, but it’s possible that it could be even better. How could we find the optimal binding sequence for this protein? Ideally, a rat...
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 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...
