How sequence alignment scores correspond to probability models.

ABSTRACT:

Motivation

Sequence alignment remains fundamental in bioinformatics. Pair-wise alignment is traditionally based on ad hoc scores for substitutions, insertions and deletions, but can also be based on probability models (pair hidden Markov models: PHMMs). PHMMs enable us to: fit the parameters to each kind of data, calculate the reliability of alignment parts and measure sequence similarity integrated over possible alignments.

Results

This study shows how multiple models correspond to one set of scores. Scores can be converted to probabilities by partition functions with a 'temperature' parameter: for any temperature, this corresponds to some PHMM. There is a special class of models with balanced length probability, i.e. no bias toward either longer or shorter alignments. The

SUBMITTER: Frith MC 

PROVIDER: S-EPMC9883716 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature