MOTIVATION Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment-in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities ...

Motivation High-throughput sequencing has transformed the study of gene expression levels through RNA-seq, a technique that is now routinely used by various fields, such as genetic research or diagnostics. The advent of third generation sequencing technologies providing significantly longer reads opens up new possibilities. However, the high error rates common to these technologies set new bioi...

An algorithm for progressive multiple alignment of sequences with insertions " , 1. Introduction The problem of sequence alignment is to find the patterns of sequence conservation and similarity between pairs or sets of given sequences. In biological contexts, similarity between biological sequences usually amounts to either functional or structural similarities or divergence from a common ance...

Coordination and harmony between different departments of a company can be an important factor in achieving competitive advantage if the company corrects alignment between strategies of different departments. This paper presents an integrated decision model based on recent advances of geometric programming technique. The demand of a product considers as a power function of factors such as produ...

This paper presents a novel optical processing approach for exploring genome sequences built upon optical correlator for global alignment and extended DV-curve method for local alignment. To overcome the problem of traditional DV-curve method for presenting an accurate and simplified output, we propose HAWPOD, built upon DVcurve method, to analyze genome sequences in five steps: DNA coding, ali...

It is a standard procedure to compare new amino acid sequences to databases of proteins that have been studied already in order to find similarities in structure and function. This comparison can be sequence–sequence or sequence– structure based. In order to compare, an alignment is performed of the target protein sequence (whose structure we are searching) with a template protein (whose struct...

This paper aims to explore the performance alignment in collaborative network environments. It has been stated that performance management based on data collection and the evaluation of key performance indicators (KPIs) may not be effective due to the different indicators and measurement systems in place for the various participants in a collaborative network (CN). Therefore, measuring the stra...

Speech-text alignment tools are frequently used in speech technology and research. In this paper, we propose a GPL software CoALT (Comparing Automatic Labelling Tools) for comparing two automatic labellers or two speech-text alignment tools, ranking them and displaying statistics about their differences. The main feature of CoALT is that a user can define its own criteria for evaluating and com...