Do you have a set of protein or polypeptide sequences (in amino acid alphabets) that you need help learning more about? Do you want to learn how to calculate the net charge, polarity, grand average of hydrophobicity, aliphatic index, average bulk, and other protein properties? Then, you have come to the right place! :) Saniya goes over how you can use the Alakazam Bioconductor package (free!) to learn more about your set of peptide sequences...it is like magic!!
Saniya reviews a few key concepts about ribosomes, amino acids (alphabet dictionary and letters), and translation to help ye better understand these concepts. Then, Saniya has an illustrative example where she uses 9 different peptide sequences (amino acids specified by a given alphabet: M is for Methionine for example): "MEPAGPAPGRLGPLLL", "MAVETRPELVGKRFLC","VAAGEDARPERGQSGCG", "RGWRAGVIRAVSHRDRG", "HPDLAVYVEFDDLEWDKR", "EWVRVYEDFSTFLVEYHLI", "WAKRKDPSQTQGSKLLCGP", "CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT".

Saniya also goes through some documentation regarding these functions.

Then, Saniya shows how the polar(), gravy(), charge(), aliphatic(), bulk() functions are used. These tools are increasingly important given shifts towards working with protein peptide array data :)

Please reach out with any questions and comments that you have. If you found this helpful, please subscribe to Saniya's YouTube channel. Thank you for your support :)

00:00 Extracting Properties of Protein/Peptide (Amino Acid) Sequences (via Alakazam Bioconductor Package)
01:45 Refresher of Biology Concepts (Proteins, Amino Acids, and Beyond)
8:08 Amino Acids can be represented by 1 letter alphabets
09:16 Loading in alakazam Bioconductor package in R
09:43 Introducing Example of several protein sequences (amino acid alphabets)
10:42 Working with alakazam to retrieve properties of these short protein sequences
11:37 calculating average polarity of protein sequences
12:10 plotting histogram in R (of the average polarity of the set of protein sequences)
12:39 using quantiles function in R to retrieve percentile information on average polarity (of the set of protein sequences)
12:55 extracting other protein properties using other functions in alakazam

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