QUESTION: "How do I do a pairwise sequence alignment in R?" If you have protein sequences from different species, how do you do a pairwise alignment to compare them in R?

If you have a protein sequence, how do you do a pairwise alignment in R?

The SLC22A5 gene provides instructions for making a protein called OCTN2 that is found in the heart, liver, muscle, kidneys, and other tissues. The gene is also known to code for a protein, solute carrier family 22 member 5. Mutations may cause systemic primary carnitine deficiency (CDSP). Sodium-ion dependent, high-affinity carnitine transporter. Involved in the active cellular uptake of carnitine. Transports one sodium ion with one molecule of carnitine. Also transports organic cations such as tetraethylammonium (TEA) without the involvement of sodium. Also, the relative uptake activity ratio of carnitine to TEA is 11.3.

Steps to adding a line of best fit to a scatterplot in ggpubr using ggscatter() function.

Amino acids can be described by a number of chemical properties. This information is fairly easy to locate for the 20 standards **proteinogenic amino acids** coded by the standard codon table. For other amino acids, it can be very difficult to find this information. A key question in the study of the origin of the universal genetic code is: of the hundreds of amino acids that occur on earth, why does the codon table code for the 20 that it does? That is, why isn't life-based on a different set of 20 amino acids? Many studies compare and contrast the chemical properties of the 20 proteinogenic amino acids with other amino acids, such as the amino acids that occur in meteorites. Unfortunately, these studies rarely publish their data. Moreover, it seems like there is not always experimentally derived data on the chemical properties of non-proteinogenic amino acids. Authors' therefore use chemistry modeling software to predict the chemical attributes of non-standard amino acids. In this portfolio assignment you will build a simple **regression model** (**line of best fit**) using the lm() function, then use the molecular weight of non-standard amino acids to predict other chemical values. You'll then assess whether this model is likely to be a very good one for predicting pI. The assignment consists only of instructions - no code! To complete this assignment, you will need to gather the necessary data and code from recent assignments to make a self-sufficient script to carry out the following analysis.

Review for Exam 4

Portfolio C