|
|
The use of numerical representations in processing of nucleotide sequences
Košíček, Adam ; Maděránková, Denisa (referee) ; Kubicová, Vladimíra (advisor)
Conversion of DNA sequences for appropriate representation is important task before initiation of analyzes and further processing. The main goal of this work was to get familiar with types of numerical and graphical representations and their application for DNA analyzes. In consideration of great volume of methods and procedures, only a few were chosen for this work. Some methods can not be classified only as numerical or graphical representations, because of option allowing them to be converted into both of these representations. These methods were classified as graphical representations. Phylogenetic trees were programmed for chosen methods to compare its precision. Outcome of this work is summing up the results.
|
|
|
Application for Visualization of Finite Automaton Structure
Polcer, Ondřej ; Horáček, Petr (referee) ; Zámečníková, Eva (advisor)
The goal of this thesis is to create an application that converts text form of a finite state machine to a state diagram. First, the code form of finite state machine syntax is transformed into the object form and complemented by additional data. The algorithm of finding appropriate placement for individual state of structure follows to make their transition clear and understandable with considering the complexity of a given finite state machine. The application creates a set of equivalent views in various form and delivers the appropriate information for easy interpretation of results.
|
|
|
Visual Representation of Pi-Calculus Expressions
Prokopová, Dagmar ; Křivka, Zbyněk (referee) ; Rychlý, Marek (advisor)
This work deals with the problem of visual representation of Pi-calculus expressions. The theoretical part of this paper discusses general principles of process algebras as well as specific properties of individual models, with a focus on Pi-calculus. Also included is the comparison of several text and graphical representations of expressions. The main part of the thesis deals with the design and implementation of an application for converting text representation of expressions into graphical representation. In addition to the text and graphical representation, an internal tree representation designed to work with expressions within the application is also proposed. The thesis also describes algorithms for finding feasible reductions, performing reductions and expression simplification that operate with the proposed tree representation.
|
|
|
Graphical representation of DNA and protein sequences
Pražák, Ondřej ; Kolářová, Jana (referee) ; Maděránková, Denisa (advisor)
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.
|
|
|
Visual Representation of Pi-Calculus Expressions
Prokopová, Dagmar ; Křivka, Zbyněk (referee) ; Rychlý, Marek (advisor)
This work deals with the problem of visual representation of Pi-calculus expressions. The theoretical part of this paper discusses general principles of process algebras as well as specific properties of individual models, with a focus on Pi-calculus. Also included is the comparison of several text and graphical representations of expressions. The main part of the thesis deals with the design and implementation of an application for converting text representation of expressions into graphical representation. In addition to the text and graphical representation, an internal tree representation designed to work with expressions within the application is also proposed. The thesis also describes algorithms for finding feasible reductions, performing reductions and expression simplification that operate with the proposed tree representation.
|
|
| |
|
|
The use of numerical representations in processing of nucleotide sequences
Košíček, Adam ; Maděránková, Denisa (referee) ; Kubicová, Vladimíra (advisor)
Conversion of DNA sequences for appropriate representation is important task before initiation of analyzes and further processing. The main goal of this work was to get familiar with types of numerical and graphical representations and their application for DNA analyzes. In consideration of great volume of methods and procedures, only a few were chosen for this work. Some methods can not be classified only as numerical or graphical representations, because of option allowing them to be converted into both of these representations. These methods were classified as graphical representations. Phylogenetic trees were programmed for chosen methods to compare its precision. Outcome of this work is summing up the results.
|
|
|
Application for Visualization of Finite Automaton Structure
Polcer, Ondřej ; Horáček, Petr (referee) ; Zámečníková, Eva (advisor)
The goal of this thesis is to create an application that converts text form of a finite state machine to a state diagram. First, the code form of finite state machine syntax is transformed into the object form and complemented by additional data. The algorithm of finding appropriate placement for individual state of structure follows to make their transition clear and understandable with considering the complexity of a given finite state machine. The application creates a set of equivalent views in various form and delivers the appropriate information for easy interpretation of results.
|
|
|
Graphical representation of DNA and protein sequences
Pražák, Ondřej ; Kolářová, Jana (referee) ; Maděránková, Denisa (advisor)
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.
|
guest ::
