Protein alignment HW/SW optimizations

Biosequence alignment recently received an amazing support from both commodity and dedicated hardware platforms. The limitless requirements of this application motivate the search for improved implementations to boost processing time and capabilities. We propose an unprecedented hardware improvement to the classic Smith-Waterman (S-W) algorithm based on a twofold approach: i) an on-the-fly gap-open/gap-extension selection that reduces the hardware implementation complexity; ii) a pre-selection filter that uses reduced amino-acid alphabets to screen out not-significant sequences and to shorten the S-Witerations on huge reference databases.We demonstrated the improvements w.r.t. a classic approach both from the point of view of algorithm efficiency and of HW performance (FPGA and ASIC post-synthesis analysis)

Complexity and modeling power of insertion-deletion systems

SISTEMAS DE INSERCIÓN Y BORRADO: COMPLEJIDAD Y CAPACIDAD DE MODELADO El objetivo central de la tesis es el estudio de los sistemas de inserción y borrado y su capacidad computacional. Más concretamente, estudiamos algunos modelos de generación de lenguaje que usan operaciones de reescritura de dos cadenas. También consideramos una variante distribuida de los sistemas de inserción y borrado en el sentido de que las reglas se separan entre un número finito de nodos de un grafo. Estos sistemas se denominan sistemas controlados mediante grafo, y aparecen en muchas áreas de la Informática, jugando un papel muy importante en los lenguajes formales, la lingüística y la bio-informática. Estudiamos la decidibilidad/ universalidad de nuestros modelos mediante la variación de los parámetros de tamaño del vector. Concretamente, damos respuesta a la cuestión más importante concerniente a la expresividad de la capacidad computacional: si nuestro modelo es equivalente a una máquina de Turing o no. Abordamos sistemáticamente las cuestiones sobre los tamaños mínimos de los sistemas con y sin control de grafo.COMPLEXITY AND MODELING POWER OF INSERTION-DELETION SYSTEMS The central object of the thesis are insertion-deletion systems and their computational power. More specifically, we study language generating models that use two string rewriting operations: contextual insertion and contextual deletion, and their extensions. We also consider a distributed variant of insertion-deletion systems in the sense that rules are separated among a finite number of nodes of a graph. Such systems are refereed as graph-controlled systems. These systems appear in many areas of Computer Science and they play an important role in formal languages, linguistics, and bio-informatics. We vary the parameters of the vector of size of insertion-deletion systems and we study decidability/universality of obtained models. More precisely, we answer the most important questions regarding the expressiveness of the computational model: whether our model is Turing equivalent or not. We systematically approach the questions about the minimal sizes of the insertiondeletion systems with and without the graph-control

Molecular Genetic Diversity Study of Forest Coffee Tree (Coffea arabica L.) Populations in Ethiopia: Implications for Conservation and Breeding

Coffee provides one of the most widely drunk beverages in the world, and is a very important source of foreign exchange income for many countries. Coffea arabica, which contributes over 70 percent of the world's coffee productions, is characterized by a low genetic diversity, attributed to its allopolyploidy origin, reproductive biology and evolution. C. arabica has originated in the southwest rain forests of Ethiopia, where it is grown under four different systems, namely forest coffee, small holders coffee, semi plantation coffee and plantation coffee. Genetic diversity of the forest coffee (C. arabica) gene pool in Ethiopia is being lost at an alarming rate because of habitat destruction (deforestation), competition from other cash crops and replacement by invariable disease resistant coffee cultivars. This study focused on molecular genetic diversity study of forest coffee populations in Ethiopia using PCR based DNA markers such as random amplified polymorphic DNA (RAPD), inverse sequence-tagged repeat (ISTR), inter-simple sequence repeats (ISSR) and simple sequence repeat (SSR) or microsatellites. The objectives of the study are to estimate the extent and distribution of molecular genetic diversity of forest coffee and to design conservation strategies for it’s sustainable use in future coffee breeding. In this study, considerable samples of forest coffee collected from four coffee growing regions (provinces) of Ethiopia were analysed. The results indicate that moderate genetic diversity exists within and among few forest coffee populations, which need due attention from a conservation and breeding point of view. The cluster analysis revealed that most of the samples from the same region (province) were grouped together which could be attributed to presence of substantial gene flow between adjacent populations in each region in the form of young coffee plants through transplantation by man. In addition wild animals such as monkeys also play a significant role in coffee trees gene flow between adjacent populations. The overall variation of the forest coffee is found to reside in few populations from each region. Therefore, considering few populations from each region for either in situ or ex situ conservation may preserve most of the variation within the species. For instance, Welega-2, Ilubabor-2, Jima-2 and Bench Maji-2 populations should be given higher priority. In addition, some populations or genotypes have displayed unique amplification profiles particularly for RAPD and ISTR markers. Whether these unique bands are linked to any of the important agronomic traits and serve in marker assisted selections in future coffee breeding requires further investigations

The genetic heritage of China: A genomic study of PR China based on nine representative ethnic populations

During the course of the last decade, genetic data have increasingly complemented linguistic, archaeological and palaeontological evidence in efforts to reconstruct human history. As technology has developed, studies have utilised genomic techniques in tracing the origins and migratory patterns of modem humans. East Asia is a particular hotspot of human migration, _especially Mainland China where a large number of human fossils have been unearthed and more than 20% of the wor1d\u27s population now resides. There are 56 officially recognised ethnic groups (minzu) within the population of PR China which totals 1,300 million. The majority Han population is distributed throughout the country and forms 90% of the total, whereas the other 55 minority populations mostly live in peripheral and boundary regions. To date, information on these minorities has been fragmentary and, from both evolutionary and historical perspectives, data on their genetic profiles would be of considerable value in identifying their founding populations and genetic inter-relationships. There are also strongly conflicting opinions on the origins of the Han and the degree to which they can be regarded as genetically homogenous. The current study measured the genetic diversity and ancestry of nine ethnic populations resident in PR China. In addition to the Han, these study populations comprised the Miao, Yao, Kucong and Tibetan communities from Yunnan province in the southwest of the country, and four Muslim populations, the Hui, Bo\u27an, Dongxiang and Sala from northern and central China. Both biparental and uniparental genetic influences on the populations were examined by the analysis of autosomal, mitochondrial and Y -chromosome markers. In general, it was found that the study populations displayed diverse paternal ancestries but more restricted maternal ancestries. From the Y-chromosome data in particular, major events such as the Neolithic population expansion and more recent historical events, such-as migration along the Silk Road, could be inferred. Through the use of autosomal markers, aspects of the internal structure of the study populations were uncovered, such as endogamy and/or consanguinity. These conclusions were made possible, in part, by experimental Likelihood-based stochastic coalescent modelling. Intriguingly. it was revealed that the Kucong of Yunnan, an ethnic group not previously surveyed for genetic diversity and not accorded official minority status within PR China. could possibly be representative of indigenous populations dating from the first migrations into East Asia. While other\u27 more recent events could be inferred from summary statistics and phylogenetic and coalescent-based genetic analyses of the study populations, the changing definition of the ethnic study populations themselves proved to be the most important factor. It is therefore recommended that future studies primarily utilize a community-by-community approach, and not rely on the official minzu category as an accurate indicator of genetic ancestry

Unity in diversity: An overview of the genomic anthropology of India

Context: India is considered a treasure for geneticists and evolutionary biologists due to its vast human diversity, consisting of more than 4500 anthropologically well-defined populations (castes, tribes and religious groups). Each population differs in terms of endogamy, language, culture, physical features, geographic and climatic position and genetic architecture. These factors contributed to India-specific genetic variations which may be responsible for various common diseases in India and its migratory populations. As a result, interpretations of the origins and affinities of Indian populations as well as health and disease conditions require complex and sophisticated genetic analysis. Evidence of ancient human dispersals and settlements is preserved in the genome of Indian inhabitants and this has been extensively analysed in conventional and genomic analyses. Objective and methods: Using genomic analyses of STRs and Alu on a set of populations, this study estimates the level and extent of genetic variation and its implications. Results: The results show that Indian populations have a higher level of unique genetic diversity which is structured by many social processes and geographical attributes of the country. Conclusion: This overview highlights the need to study the anthropological structure and evolutionary history of Indian populations while designing genomic and epigenomic investigations. © 2014 Informa UK Ltd