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...

Poxvirus Orthologous Clusters (POCs) is a JAVA client-server application which accesses an updated database containing all complete poxvirus genomes; it automatically groups orthologous genes into families based on BLASTP scores for assessment by a human database curator. POCs has a user-friendly interface permitting complex SQL queries to retrieve interesting groups of DNA and protein sequence...

To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions for measuring alignment quality. In this paper, we introduce probabilistic consist...

Phylogenetic analysis based on alignment method meets huge challenges when dealing with whole-genome sequences, for example, recombination, shuffling, and rearrangement of sequences. Thus, various alignment-free methods for phylogeny construction have been proposed. However, most of these methods have not been implemented as tools or web servers. Researchers cannot use these methods easily with...

Resources for evaluating sentence-level and word-level alignment algorithms are unsatisfactory. Regarding sentence alignments, the existing data is too scarce, especially when it comes to difficult bitexts, containing instances of non-literal translations. Regarding word-level alignments, most available hand-aligned data provide a complete annotation at the level of words that is difficult to e...

In terms of sustainability, traditional disclosure does not provide the necessary information to all stakeholders, mainly addressing company’s shareholders’ expectations. As a result, organisations need disclose more non-financial information, which implies social and environmental issues. Many currently sustainability reports in addition annual management containing financial economic data. Se...

The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel tree...

We present a semi-supervised, languageand domain-independent approach to high precision sentence alignment. The key idea is to bootstrap a supervised discriminative learner from wood-standard alignments, i.e. alignments that have been automatically generated by state-ofthe-art sentence alignment tools. We deploy 3 different unsupervised sentence aligners (Opus, Hunalign, Gargantua) and 2 differ...

SUMMARY We developed PSAR-Align, a multiple sequence realignment tool that can refine a given multiple sequence alignment based on suboptimal alignments generated by probabilistic sampling. Our evaluation demonstrated that PSAR-Align is able to improve the results from various multiple sequence alignment tools. AVAILABILITY AND IMPLEMENTATION The PSAR-Align source code (implemented mainly in ...