I have a file of Data includes 20 proteins, each 10 proteins belongs to different class. My goal is to extract the similarities among 10 sequences and between those two classes in Protein level and RNA level. So, I reversed them to RNA code and I saved them in different file. I want to analysis both files of protein and RNA to find some similarity regions that may RNA share it in each class, and repeat the same thing in Protein. Firstly, I use local multiple sequence alignment of 10 RNA sequences by MUSCLE , and I used Jalview program for this purpose. Jalviews shows me some coloured area that have the same percentage of identity.
My question is:
I would like to represent these colours by numbers, but Jalview didn't give me any score or numbers to find the percentage of identity.. !! How I can analysis my data to extract the similarities among sequences of both class and both level of gene (RNA and Protein) ? And how I can represent them by quantitative measurement (e.g. similarity score, level of variation, percentage of identity) or you can suggest me another type of measurement ?