Interpreting alignment-free sequence comparison: what makes a score a good score?

ABSTRACT: Alignment-free methods are alternatives to alignment-based methods when searching sequence data sets. The output from an alignment-free sequence comparison is a similarity score, the interpretation of which is not straightforward. We propose objective functions to interpret and calibrate outputs from alignment-free searches, noting that different objective functions are necessary for different biological contexts. This leads to advantages: visualising and comparing score distributions, including those from true positives, may be a relatively simple method to gain insight into the performance of different metrics. Using an empirical approach with both DNA and protein sequences, we characterise different similarity score distributions generated under different parameters. In particular, we d

SUBMITTER: Swain MT 

PROVIDER: S-EPMC9442500 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature