Szerző szerinti böngészés "Karimi, Ramin"
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Tétel Korlátozottan hozzáférhető A comparative study of genome databases(2012-05-30T10:11:25Z) Karimi, Ramin; Hajdú, András; DE--TEK--Informatikai KarThe rapid increasing in the number of fully sequenced genomes of numerous species and massive amounts of data generated by molecular biology and biochemistry creates new opportunities for comparative studies. This achievement combined with the progress in computational tools and applications that occurred in the last few decades allowed the use of new approaches in the study of genome databases. Numerous biological databases and computational tools have been created attempting to optimize the access to this information through the web. There are two types of databases: First local database that records internal data from that laboratory’s experiments and second, public database accessed through the Internet, such as NCBI, GenBank, EBI and EMBL. The genome sequences and various numbers of databases are available to anyone with Internet access. In this thesis, I present the main public databases, resources, different data formats and computational tools and applications available through the web for comparative analysis of genomic and proteomic sequences and other molecular biology datasets to support current interests in this field.Tétel Szabadon hozzáférhető Computational Methods and Applications for Real-Time Identification of Species and Pathogens from Raw Read Sequencing Data.Karimi, Ramin; Hajdu, András; Informatikai tudományok doktori iskola; DE--Informatikai Kar -- Department of Computer Graphics and Image ProcessingA very small proportion (often cited as <1%) of the total microbial diversity in nature can be cultivated in the laboratory. The vast majority of them cannot be isolated or are extremely difficult to grow in the laboratory. In recent years, impressive progress has been made in the field of bioinformatics by technological advances of genome sequencing to perform whole genome sequencing in thousands of individuals. The emerging field of metagenomics provides a series of technical innovations for culture-independent scrutiny of microbial communities in the environment. It is a large-scale sequencing of the entire community, sampled directly from its natural environment. It provides new opportunities for gaining access to previously hidden phylogenetic, functional, metabolic, and ecological diversity of organisms and their community structure. While these technologies are constantly continued to offer increases in throughput, the time and cost of DNA sequencing continue to fall. Therefore, sequencing technologies are becoming applicable as a routine tool for diagnostic and public health microbiology. However, the complexity of the analysis and high-costs of the computational resources has encountered many challenges and obstacles to achieving this goal. One of the major challenges for metagenomics studies is the accurate identification of organisms present in complex environments. Although, a wide variety of assembling and alignment-based algorithms, software and computational analysis workflows have been subsequently developed, computational approaches for alignment-based identification of complex communities, without very extensive sequencing coverage are inadequate for even the most abundant members. In this research, we have proposed an alignment-free method and its appropriate pipelines and software for Real-time identification of species and strains from raw read sequencing data. The method tries to shortcut identification into a quick and accurate process in environmental and clinical sequencing samples, using parallel and distributed computing on commodity hardware for enhancing the applicability of the analysis as a routine process in the entire research community.Tétel Szabadon hozzáférhető HTSFinder: Powerful pipeline of DNA signature discovery by parallel and distributed computing(2016) Karimi, Ramin; Hajdu, András