Browsing by Author "Carvalho, Paulo"
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- DC: a highly efficient and flexible exact pattern-matching algorithmPublication . Deusdado, Sérgio; Carvalho, Pauloware of the need for faster and flexible searching algorithms in fields such as web searching or bioinformatics, we propose DC - a high-performance algorithm for exact pattern matching. Emphasizing the analysis of pattern peculiarities in the pre-processing phase, the algorithm en- compasses a novel search logic based on the examination of multiple alignments within a larger window, selectively tested after a powerful heuristic called compatibility rule is verified. The new algorithm’s performance is, on average, above its best-rated competitors when testing different data types and using a complete suite of pattern extensions and compositions. The flexibility is remarkable and the efficiency is more relevant in quaternary or greater alphabets. Keywords: exact pattern-match, searching algorithms.
- Efficient exact pattern-matching in proteomic sequencesPublication . Deusdado, Sérgio; Carvalho, PauloThis paper proposes a novel algorithm for complete exact pattern-matching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A new filtering heuristic, named compatibility rule, contributed decisively to the efficiency improvement. The new algorithm’s performance is, on average, superior in comparison with its best-rated competitors.
- Employing compact intra-genomic language models to predict genomic sequences and characterize their entropyPublication . Deusdado, Sérgio; Carvalho, PauloProbabilistic models of languages are fundamental to understand and learn the profile of the subjacent code in order to estimate its entropy, enabling the verification and prediction of “natural” emanations of the language. Language models are devoted to capture salient statistical characteristics of the distribution of sequences of words, which transposed to the genomic language, allow modeling a predictive system of the peculiarities and regularities of genomic code in different inter and intra-genomic conditions. In this paper, we propose the application of compact intra-genomic language models to predict the composition of genomic sequences, aiming to achieve valuable resources for data compression and to contribute to enlarge the similarity analysis perspectives in genomic sequences. The obtained results encourage further investigation and validate the use of language models in biological sequence analysis.
- GRASPm: an efficient algorithm for exact pattern-matching in genomic sequencesPublication . Deusdado, Sérgio; Carvalho, PauloIn this paper, we propose Genomic-oriented Rapid Algorithm for String Pattern-match (GRASPm), an algorithm centred on overlapped 2-grams analysis, which introduces a novel filtering heuristic – the compatibility rule – achieving significant efficiency gain. GRASPm’s foundations rely especially on a wide searching window having the central duplet as reference for fast filtering of multiple alignments. Subsequently, superfluous detailed verifications are summarily avoided by filtering the incompatible alignments using the idcd (involving duplet of central duplet) concept combined with pre-processed conditions, allowing fast parallel testing for multiple alignments. Comparative performance analysis, using diverse genomic data, shows that GRASPm is faster than its competitors.
- QoS adaptation in multimedia multicast conference applications for e-learning servicesPublication . Deusdado, Sérgio; Carvalho, PauloTolerant real-time applications, such as video conferences, are in the frontline to benefit from QoS adaptation. However, not all include adaptive technology able to provide both end-system and network quality awareness. Adaptation, in these cases, can be achieved by introducing a multiplatform middleware layer responsible for tutoring the applications’ resources (enabling adjudication or limitation) based on the available processing and networking capabilities. Congregating these technological contributions, an adaptive platform has been developed integrating public domain multicast tools, applied to a Web-based distance learning system. The system is user-centered (estudent), aiming at good pedagogical practices and proactive usability for multimedia and networkresources. The services provided, including QoS adapted interactive multimedia multicast conferences (MMC), are fully integrated and transparent to end-users. QoS adaptation, when treated systematically in tolerant real-time applications, denotes advantages in group scalability and QoS sustainability in heterogeneous and unpredictable environments such as the Internet.
- QoS adaptation in multimedia multicast conference applications for E-learning servicesPublication . Deusdado, Sérgio; Carvalho, PauloThe evolution of the World Wide Web service has incorporated new distributed multimedia conference applications, powering a new generation of e-learning development and allowing improved interactivity and prohuman relations. Groupware applications are increasingly representative in the Internet home applications market, however, the Quality of Service (QoS) provided by the network is still a limitation impairing their performance. Such applications have found, in multicast technology, an ally contributing for their efficient implementation and scalability. Additionally, considering QoS as a design goal at the application level becomes crucial for groupware development, enabling QoS productivity to applications. The applications’ ability to adapt themselves dynamically according to the resources availability can be considered a quality factor.Tolerant real-time applications, such as video conferences, are in the frontline to benefit from QoS adaptation. However, not all include adaptive technology able to provide both end-system and network quality awareness. Adaptation, in these cases, can be achieved by introducing a multiplatform middleware layer responsible for tutoring the applications’ resources (enabling adjudication or limitation) based on the available processing and networking capabilities. Congregating these technological contributions, an adaptive platform has been developed integrating public domain multicast tools, applied to a Web-based distance learning system. The system is user-centered (e-student), aiming at good pedagogical practices and proactive usability for multimedia and network resources. The services provided, including QoS adapted interactive multimedia multicast conferences (MMC), are fully integrated and transparent to end-users. QoS adaptation, when treated systematically in tolerant real-time applications, denotes advantages in group scalability and
- Scrapie at abattoir: monitoring, control, and differential diagnosis of wasting conditions during meat inspectionPublication . Esteves, Alexandra; Vieira-Pinto, Madalena; Quintas, Helder; Orge, Leonor; Gama, Adelina; Alves, Anabela; Seixas, Fernanda; Pires, Isabel; Pinto, Maria de Lurdes; Mendonça, Ana Paula; Lima, Carla; Machado, Carla Neves; Silva, João Carlos; Tavares, Paula; Silva, Filipe; Bastos, Estela; Pereira, Jorge; Gonçalves-Anjo, Nuno; Carvalho, Paulo; Sargo, Roberto; Matos, Ana; Figueira, Luís; Pires, Maria dos AnjosWasting disease in small ruminants is frequently detected at slaughterhouses. The wasting disorder is manifested by the deterioration of the nutritional and physiological state of the animal indicated by thinness, emaciation, and cachexia. Evidence of emaciation and cachexia, alone, are pathological conditions leading to carcass condemnation during an inspection. Several diseases are associated with a wasting condition, including scrapie, pseudotuberculosis, tuberculosis, paratuberculosis, Maedi Visna, and tumor diseases. On the other hand, parasitic diseases, nutrition disorders, exposure or ingestion of toxins, metabolic conditions, inadequate nutrition due to poor teeth, or poor alimentary diet are conditions contributing to poor body condition. Classical and atypical scrapie is naturally occurring transmissible spongiform encephalopathies in small ruminants. The etiological agent for each one is prions. However, each of these scrapie types is epidemiologically, pathologically, and biochemically different. Though atypical scrapie occurs at low incidence, it is consistently prevalent in the small ruminant population. Hence, it is advisable to include differential diagnosis of this disease, from other possibilities, as a cause of wasting conditions detected during meat inspection at the abattoir. This manuscript is a review of the measures in force at the abattoir for scrapie control, focusing on the differential diagnosis of gross lesions related to wasting conditions detected in small ruminants during meat inspection.
- SimSearch: A new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequencesPublication . Deusdado, Sérgio; Carvalho, PauloIn this paper, we propose SimSearch, an algorithm implementing a new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences. The initial phase of SimSearch is devoted to fulfil the binary similarity matrices by signalling the distances between occurrences of the same symbol. The scoring scheme is further applied, when analysed the maximal extension of the pattern. Employing bit parallelism to analyse the global similarity matrix’s upper triangle, the new methodology searches the sequence(s) for all the exact and approximate patterns in regular or reverse order. The algorithm accepts parameterization to work with greater seeds for near-optimal results. Performance tests show significant efficiency improvement over traditional optimal methods based on dynamic programming. Comparing the new algorithm’s efficiency against heuristic based methods, equalizing the required sensitivity, the proposed algorithm remains acceptable.
- Synchronous e-learning integrating multicast applications and adaptive QOSPublication . Deusdado, Sérgio; Carvalho, PauloA new generation of e-learning development, based on synchronous groupware applications integration, providing improved interactivity and pro-human relations, allows richer training experiences far beyond a virtual classroom. Despite WWW service evolution, e-conferencing multimedia applications remain “killer applications” and insensitive to resources degradation, in fact, the quality of service (QoS) provided by the network is still a limitation impairing their performance. Such applications have found in multicast technology an ally contributing for their efficient implementation and scalability. Additionally, considering QoS as design goal at application level becomes crucial for groupware development, enabling QoS proactivity to applications. The applications’ ability to adapt themselves dynamically according to the resources availability can be considered a quality factor. Tolerant real-time applications, such as videoconferences, are in the frontline to benefit from QoS adaptation. However, not all include adaptive technology is able to provide both end-system and network quality awareness. Adaptation, in these cases, can be achieved by introducing a multiplatform middleware layer responsible for tutoring the applications’ resources (enabling adjudication or limitation) based on the available processing and networking capabilities. Congregating these technological contributions, an adaptive platform has been developed integrating public domain multicast tools, applied to a Web-based distance learning system. The system is user-centered (e-student), aiming at good pedagogical practices and proactive usability for multimedia and network resources. The services provided, including QoS adapted interactive multimedia multicast conferences (MMC), are fully integrated and transparent to end-users. QoS adaptation, when treated systematically in tolerant real-time applications, denotes advantages in group scalability and QoS sustainability in heterogeneous and unpredictable environments such as the Internet.