A phylogenetic approach for weighting genetic sequences.

ABSTRACT:

Background

Many important applications in bioinformatics, including sequence alignment and protein family profiling, employ sequence weighting schemes to mitigate the effects of non-independence of homologous sequences and under- or over-representation of certain taxa in a dataset. These schemes aim to assign high weights to sequences that are 'novel' compared to the others in the same dataset, and low weights to sequences that are over-represented.

Results

We formalise this principle by rigorously defining the evolutionary 'novelty' of a sequence within an alignment. This results in new sequence weights that we call 'phylogenetic novelty scores'. These scores have various desirable properties, and we showcase their use by considering, as an example application, the inferenc

SUBMITTER: De Maio N 

PROVIDER: S-EPMC8164272 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature