To study evolution on the genetic level across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Given a set of biological sequences, a multiple alignment provides biologists with a way of identifying and visualizing patterns of sequence conservation, advancing both evolutionary and phylogenetic studies. Protein alignments in particul...

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequencelength requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is distance-based, that is, it relies on pairwise sequence comparisons. More importantly, our approach largely bypasses the difficult problem of multiple sequence alig...

In this study we apply and evaluate an iterative pairwise alignment program for producing multiple sequence alignments, ALPHAMALIG (Alonso et al., 2004), using as material the phonetic transcriptions of words used in Bulgarian dialectological research. To evaluate the quality of the multiple alignment, we propose two new methods based on comparing each column in the obtained alignments with the...

We care about the sequence alignments in the computational biology because it gives biologists useful information about different aspects. For example, it can tell us about the evolution of the organisms, we can see which regions of a gene (or its derived protein) are susceptible to mutation and which can have one residue replaced by another without changing function, we can study Homologous ge...

The multiple sequence alignment problem (MSA) can be reformulated as the problem of finding a maximum weight trace in an alignment graph, which is derived from all pairwise alignments. We improve the alignment graph by adding more global information. A new construction heuristic and an evolutionary algorithm with specialized operators are proposed and compared to three other algorithms for the ...

This paper presents a discriminative alignment model for extracting abbreviations and their full forms appearing in actual text. The task of abbreviation recognition is formalized as a sequential alignment problem, which finds the optimal alignment (origins of abbreviation letters) between two strings (abbreviation and full form). We design a large amount of finegrained features that directly e...

In this paper, we show how to form Partial-Order Multiple-Sequence Alignment graphs on two types of reconfigurable mesh architectures. The first reconfigurable mesh is a standard micro-scale one that uses electrical interconnects, while the second one can be implemented at a nano-scale level and employs spin waves for interconnectivity. We consider graph formations for two cases. In one case, t...