We develop a novel and general approach to estimating the accuracy of multiple sequence
alignments without knowledge of a reference alignment, and use our approach to address a …

Background A standard procedure in many areas of bioinformatics is to use a single multiple
sequence alignment (MSA) as the basis for various types of analysis. However, downstream …

This book develops a new approach called parameter advising for finding a parameter
setting for a sequence aligner that yields a quality alignment of a given set of input …

While the multiple sequence alignment output by an aligner strongly depends on the
parameter values used for the alignment scoring function (such as the choice of gap …

Proteins are biological molecules that carry out a multitude of cellular functions. Their
function is largely determined by the shape of the folded molecule within the cell—called …

Background While the multiple sequence alignment output by an aligner strongly depends
on the parameter values used for its alignment scoring function (ie choice of gap penalties …

The multiple sequence alignments computed by an aligner for different settings of its
parameters, as well as the alignments computed by different aligners using their default …

While the multiple sequence alignment output by an aligner strongly depends on the
parameter values used for the alignment scoring function (such as the choice of gap …

Protein secondary structure prediction is a fundamental task in computational biology, basic
to many bioinformatics workflows, with a diverse collection of tools currently available. An …

In a computed protein multiple sequence alignment, the coreness of a column is the fraction
of its substitutions that are in so-called core columns of the gold-standard reference …