Improvements in the score matrix calculation method using parallel score estimating algorithm

The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.

Relatório de projecto

Relatório de Projecto no âmbito do Mestrado em Tradução e Interpretação Especializadas, sob orientação da Professora Doutora Clara Sarmento.

Traducción médica comentada inglés-español: Polycystic Ovary Syndrome(Joyce King)

El trabajo se divide en tres partes: una traducción del ámbito médico inglés-español; un glosario de términos extraídos del texto con su equivalente en español, y un análisis de los principales problemas de traducción detectado y que son frecuentes en los textos biomédicos, con sus respectivas soluciones.

Traducción comentada de «Management of the Clinically Positive Axilla» y «Management of the Internal Mammary Lymph Nodes», Essentials of Breast Surgery

La transmisión de conocimiento científico constituye una de las necesidades de traducción más importantes; es preciso realizar un estudio sobre la traducción del inglés médico. Este trabajo presenta una traducción inédita de fragmentos de Essentials of Breast Surgery y un análisis de esta jerga mediante un glosario y problemas de traducción.

Algo que se ha descuidado en el problema de la educación; un côté négligé dans le problème de l'educacion

Parallel texts in Spanish and French.

Contestación de d. Raimundo Miguel

Parallel texts of P. Polo's Notas criticas and the author's reply.

Desiderii Era[smi] Roterodami Colloquia familiaria nonnulla selecta, or, Some select familiar colloquies of D. Erasmus of Rotterdam : with a literal translation /

Parallel texts in Latin and English.

Lichtenberg: a doctrine of scattered occasions; reconstructed from his aphorisms and reflections.

"All quotations are in English, parallel texts in German are given wherever ... [required]"

Oeuvres d'Ausone,

Latin and French parallel texts.

The lament of Tasso; supposed to have been written in the dungeon of the lunatic hospital at Ferrara ...

Dutch translation by J. van Lennep.

The plays of Molière in French,

Parallel texts.

Cornelii Nepotis Vitæ excellentium imperatorum: cum versione anglicanâ ... or, Cornelius Nepos's Lives of the excellent commanders,

Parallel texts in Latin and English.

Assessment of the EEE-4 oral test: a discourse analysis based on complex networks.

With the development of information technology, the theory and methodology of complex network has been introduced to the language research, which transforms the system of language in a complex networks composed of nodes and edges for the quantitative analysis about the language structure. The development of dependency grammar provides theoretical support for the construction of a treebank corpus, making possible a statistic analysis of complex networks. This paper introduces the theory and methodology of the complex network and builds dependency syntactic networks based on the treebank of speeches from the EEE-4 oral test. According to the analysis of the overall characteristics of the networks, including the number of edges, the number of the nodes, the average degree, the average path length, the network centrality and the degree distribution, it aims to find in the networks potential difference and similarity between various grades of speaking performance. Through clustering analysis, this research intends to prove the network parameters’ discriminating feature and provide potential reference for scoring speaking performance.

Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

Using Threads to Overcome Synchronization Delays in Parallel Multiple Progressive Alignment Algorithms

Sao Paulo State Research Foundation-FAPESP