Repetition-free Longest Common Subsequence as similarity measure I'm starting a thesis in Computer Science with topic the RFLCS (Repetition-free Longest Common Subsequence). I know very little about Bioinformatics problems and Genomics. I would like to understand the motivations behind this problem.
More precisely, I'd like to understand why one need a similarity measure between genomes, and how the RFLCS is an useful measure.

[Adi et al.] introduce the problem in this article.
A brief literature review can give you the answers.

This preprint gives the definition of RFLCS more clearly:


  A repetition free Longest Common Subsequence (LCS) of two sequences x and y is an LCS of x and y where each symbol may appear at most once.


Adi et al proposed to solve the genome rearrangement problem raised in this paper. If you want to know more, follow the references and citations of these papers and read them.

Basically, Adi et al think the length of RFLCS measures the distance between two genomes. The longer the more similar. I am not sure if this is a good measurement, though.