Just college student taking upper division lab in bioinformatics, not sure if its okay to post questions like this on this forum, if not then I will not post anymore just let me know please!
I am hoping some of the questions below are familiar to you guys
So we did a lab that went over hydrophobicity plotting and we did that by plugging a protein sequence into Protscale (not sure if you have used this website before) and then it would give us a hydrophobicity plot and I just wanted to double check some of my answers. Also we did a Chou-Fasman plot of a different protein sequence (basically the Chou-Fasman algorithm predicts protein secondary structure based on primary sequence). Anyways I only have 3 questions just wanted to double check, they don't necessarily have much to do with understanding these different scales but more about reading different plots because I am not so good at reading plots to be honest.
1) Here is a plot using Kyte-Doolittle and Eisenberg hydrophobicity scale of the same protein sequence. How do they compare in terms of transmembrane predictions?
Here is Kyte-Doolitte scale: https://imgur.com/yqGCEqO
Here is Eisenberg scale: https://imgur.com/QowwqJ1
The obvious thing is that the plots look fairly similar its just that the scaling in Eisenberg is different however you can still tell which regions are hydrophobic and which ones are hydrophilic, thoughts on my answer?
2) We also used the same sequence and inserted it into TMHMM. How does the TMHMM plot compare to the Kyte-Doolitte scale and Eisenberg scale above?
Here is the TMHMM plot by the way: https://imgur.com/vcGrf48
The obvious one is that the TMHMM plot uses probability of trans-membrane helices in proteins instead of free energy y axis in the other graphs. Also it kind of looks at a protein in terms of a cell that include intra and extracellular instead of just peaks. It shows what parts are inside the cell and are hydrophobic and which parts are outside the cell and are hydrophilic, what you think about this answer?
3) For final question I am being asked to use a protein sequence and use the Chou-Fasman alpha-helical predictions. ANYWAYS I am being asked to to analyze the plot of the Chou-Fasman and the question is how many regions exceed a threshold of 1.1?
Here is the Chou-Fasman plot: https://imgur.com/qoIpwdz
My answer is that the only region that exceeds 1.1 is only 1 region and its between positions 120 ish to 145 ish, thoughts?
Thanks guys! Again you don't need to know the stuff I am talking about but mainly just comparing the plots if you are not familiar with this then no problem!
