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1	STAIRS : Data reduction strategy on genomics Ferrer, Samuel January 2019 (has links) Background. An enormous accumulation of genomic data has been taking place over the last ten years. This makes the activities of visualization and manual inspection, key steps in trying to understand large datasets containing DNA sequences with millions of letters. This situation has created a gap between data complexity and qualified personnel due to the need of trading between visualization, reduction capacity and exploratory functions, features rarely achieved by existing tools, such as SRA toolkit (https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/), for instance. A novel approach to the problem of genomic analysis and visualization was pursued in this project, by means of STrAtified Interspersed Reduction Structures (STAIRS). Result. Ten weeks of intense work resulted in novel algorithms to compress data, transform it into stairs vectors and align them. Smith–Waterman and Needleman–Wunsch algorithms have been specially modified for this purpose and the application brought about statistical performance and behavioural charts. Waterman Needleman Alignment Topology Statistics Functional Mathematics Microbiology genomics bacillus frequency analysis Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi)
2	Grafická reprezentace genomických a proteomických sekvencí / Graphical representation of DNA and protein sequences Pražák, Ondřej January 2011 (has links) Modification of DNA sequences and their suitable representation is important part of analysis, comparison and another processing. Goal of this paper is finding of suitable methods for representation of genomic and proteomic sequences. Because there is great number of metods, this paper will introduce only some of them. All selected methods, are described in the first part of this paper and they were programed in Matlab. Selected methods are illustrated on coding sequences of the first exon of the b-globin gene of 11 different species. Results are compared withresults from the original papers. Some methods are capable of another processing like cluster analysis. Output of this paper is comparison of results, gained from different methods, and finding the most suitable one.
3	Locally enhanced voronoi cell finite element model (LE-VCFEM) for ductile fracture in heterogeneous cast aluminum alloys Hu, Chao 07 January 2008 (has links) No description available. Engineering, Mechanical Voronoi cell finite element model Ductile fracture Matrix cracking Void coalescence
4	Techniques for Storing and Processing Next-Generation DNA Sequencing Data Camerlengo, Terry Luke 02 June 2014 (has links) No description available. Bioinformatics DNA sequence storage 4 bit encoding reference-based compression Needleman-Wusnch DNA base pair compression sequence compression MongoDB NGS Data management bioinformatics NoSQL 3 bases per byte
5	Shlukování proteinových sekvencí na základě podobnosti primární struktury / Clustering of Protein Sequences Based on Primary Structure of Proteins Jurásek, Petr January 2009 (has links) This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.
6	Určování genetické odlišnosti biologických sekvencí DNA / Determination of genetic differences of biological DNA sequences Sliž, Ladislav Unknown Date (has links) Work on determining the genetic diversity of biological signal aligning DNA sequences, will address a brief description of the composition of DNA. Following is basic information on the bioinformatics analysis. Then the work will describe the possibility of aligning DNA sequences. Work will focus primarily on global Needleman-Wunsch algorithm and local Smit - Watermanovův algorithm. Furthermore, this work will focus on aligning DNA sequences using methods CGR and FCGR. At the end of the work will describe the practical application of identifying genetic differences by aligning the sequences.
7	Implementace algoritmu pro hledání podobností DNA řetězců v FPGA / Approximate String Matching Algorithm Implementation in FPGA Pařenica, Martin January 2007 (has links) This paper describes sequence alignment algorithms of nucleotide sequences. There are described pairwise alignment algorithms using database search or dynamic programming. Then in the paper is description of dynamic programming for multiple sequences and algorithm that builds phylogenetic trees. At the end of the first part of the paper is the description of technology FPGA. In the second part that is more practical is described implemntation of the choosen one algorithm. This part includes also examples of some multiple alignments.
8	Hardwarová akcelerace algoritmu pro hledání podobnosti dvou DNA řetězců / Hardware Acceleration of Algorithms for Approximate String Matching Nosek, Ondřej January 2007 (has links) Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.

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