Adaptive Local Realignment of Protein Sequences

Boosting Alignment Accuracy by Adaptive Local Realignment

While mutation rates can vary markedly over the residues of a protein, multiple sequence alignment tools typically use the same values for their scoring-function parameters across a protein’s entire length. We present a new approach, called adaptive local realignment, that in contrast automatically adapts to the diversity of mutation rates along protein sequences. This builds upon a recent tech...

Boosting alignment accuracy through adaptive local realignment

Motivation: While mutation rates can vary across the residues of a protein, when computing alignments of protein sequences the same setting of values for substitution score and gap penalty parameters is typically used across their entire length. We provide for the first time a new method called adaptive local realignment that automatically uses diverse parameter settings in different regions of...

On Reducing sequences and an Application to Local Cohomology Modules

Local multiple alignment of numerical sequences: detection of subtle motifs from protein sequences and structures.

This paper presents a new method to find motifs from multiple protein sequences and multiple protein structures. The method consists of two parts: quantification and local multiple alignment. In the former part, protein sequences and protein structures are transformed into sequences of real numbers and real vectors respectively. In the latter part, fixed length regions having similar shapes are...

CRANN: detecting adaptive evolution in protein-coding DNA sequences

A software program CRANN has been developed in order to detect adaptive evolution in protein-coding DNA sequences.