Multiple sequence alignment (MSA) is widely used to reveal structural and functional changes leading to genetic differences among species, and to reconstruct evolutionary histories of related genes, proteins and genomes. Traditionally, proteins and their coding sequences (CDSs) are aligned and analyzed separately, but often drastically different conclusions were drawn on a same set of data. Her...

As the sequence identity between a pair of proteins decreases, alignment strategies that are based on sequence and/or sequence profiles become progressively less effective in identifying the correct structural correspondence between residue pairs. This significantly reduces the ability of comparative modelingbased approaches to build accurate structural models. Incorporating into the alignment ...

A new evolutionary-progressive method for Multiple Sequence Alignment problem is proposed. The method efficiently combines flexibility of evolutionary approach with speed and accuracy of progressive technique. The results show that the hybrid method is an interesting alternative for purely genetic or purely progressive approaches.

Motivation:

This paper analyzes the computational complexity of computing the optimal alignment of a set of sequences under the SP (sum of all pairs) score scheme. We solve an open question by showing that the problem is NP -complete in the very restricted case in which the sequences are over a binary alphabet and the score is a metric. This result establishes the intractability of multiple sequence alignm...

Knowledge creation entails collaborative learning processes, involving groups of students that act collaboratively in order to create new knowledge. In this study, we discuss shared epistemic agency as one of the main concepts capturing the process and evolution of collaboratively creating knowledge. A multiple-method approach was employed when analyzing the data collected from a research modul...

The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of 5 years ago. As increasing amounts of sequence dat...

The phenomenon of concentration of measure on high dimensional structures is usually stated in terms of a metric space with a Borel measure, also called an mm-space. We extend some of the mm-space concepts to the setting of a quasi-metric space with probability measure (pq-space). Our motivation comes from biological sequence comparison: we show that many common similarity measures on biologica...

We study sums S = S(d, n, k) = ∑ j≥1 [ d] jk( j )j! with d ∈ N = {1, 2, . . . } and n, k ∈ N0 = {0, 1, 2, . . . } and relate them to (finite) multiple zeta functions. As a byproduct of our results we obtain asymptotic expansions of ζ(d + 1) −H n as n tends to infinity. Furthermore, we relate sums S to Nielsen’s polylogarithm.