For my master's thesis in bioinformatics, I am trying to study the evolution of genes associated with phenotypes having strong evidence of functional between them,like sleep ----circadian rhythms--- memory consolidation. I request not only the experts of related fields to help me with my query,but also people who are building their own base in my chosen area of interest.
I believe there are 2 parts which will be integral before and during my reserach(please share your perspectives, if there are more which I might have missed)-
- To explore and formulate a certain logical pathway on how to answer the questions related to their evolution (for example, whether in all the mammalian species we currently know , the genes associated with the phenotypes were co-evolving or not and whether the rates of such phenomenon deviates from species to species)by understanding and combining core biological concepts.
- The identification and the potential development of bioinformatic tools and databases to address the above point.
So hence, I need some help in asking the right questions and trying to find a sense of direction, which I can follow so as to try to solve such interesting questions.
Reference papers, articles, books, names of bioinformatics tools and pipelines, some wacky tips and tricks are all welcome
Right now, I am trying and have tried to form my dataset ,by collect the list of genes associated with each of the 3 phenotypes discussed above from Homo sapiens(from literature). I am also collecting all the known mammalian orthologues of the same gene, and am planning to use some Metatherians as my out group for evolutionary comparisons. I am convinced that I am not formulating my dataset properly , I feel like I am missing out on something, for example,I am not sure whether to take only CDS sequences or the whole gene.I really want to know how do people working in such areas ask and formulate questions in their area, how do they find the sense of direction which they want to follow to address their reserach problem