|
|
Genomic Data Mining Techniques
Jaša, Petr ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.
|
|
|
Alignment of DNA Parts
Pejř, Václav ; Burgetová, Ivana (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with finding the possibilities within the sphere of alignment of DNA sequences. Based on these findings, the best solution should be found with regard to the quickness of computation and quality of alignment. Following this I intend to implement and thus create a functioning program that will do the alignment. The thesis starts with introducing issues dealing with biology, DNA and genetics. The introduction is followed by a survey of algorithms that are used for alignment, their evaluation and selection of the most appropriate algorithm for the implementation. The thesis also focuses on the usage of parallel programming by means of OpenCL libraries. The alignment is being done above many sequences at the same time, so that the methods how this process can be done and how to reach the best results are being examined.
|
|
|
Identifying CpG islands in genomes of eukaryotes
Urbánková, Kateřina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with searching CpG islands in DNA. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There is basic information about human and chimpanzees genome and specification of CpG islands. Practical part consists of a program that searches for CpG islands in sequences, it displayes and saves it. This work includes analysis of genes which are common for Homo sapiens, Pan troglodytes, Mus musculus and Bos taurus.
|
|
|
Detection of DNA/RNA fragments using graphene sensor and influence of upper electrolytic gate
Herzánová, Kristína ; Konečný, Martin (referee) ; Bartošík, Miroslav (advisor)
Jedinečné vlastnosti grafenu, jako je biokompatibilita, vysoká mobilita nosičů náboje a povrchová citlivost, z něj činí vhodný materiál pro biosenzory. Cílem této práce je popsat a představit takové senzory a měření provedená za účelem detekce fragmentů DNA, konkrétně látek na bázi cytosinu. Grafen je v polem řízených tranzistorech zapojen jako vodivý snímající kanál. Dopování grafenu vyvolané adsorpcí molekul na vodivém kanálu způsobuje změny transportních vlastností grafenu. Tyto změny se odrážejí v měření elektronických odezev: měření odporu grafenové vrstvy reagujícího v reálném čase na přidávání různých roztoků a závislost odporu na průběžné změně hradlového napětí. Druhou metodu měření lze provádět FET senzorem zapojeným v konfiguraci se spodním nebo elektrolytickým horním hradlem. Je sledován rozdíl mezi oběma konfiguracemi a také vliv vzdálenosti mezi grafenem a horní hradlovou elektrodou na odezvu senzoru. Výsledkem těchto měření jsou transferové křivky vykazující typické píky označující bod neutrality (Diracův bod) grafenu. Různé koncentrace roztoku analytu vedou k různým hodnotám napětí Diracova bodu, což slouží ke kvantifikaci úrovně dopování grafenu.
|
|
|
Detection of DNA/RNA fragments using graphene sensor and influence of upper electrolytic gate
Herzánová, Kristína ; Konečný, Martin (referee) ; Bartošík, Miroslav (advisor)
Jedinečné vlastnosti grafenu, jako je biokompatibilita, vysoká mobilita nosičů náboje a povrchová citlivost, z něj činí vhodný materiál pro biosenzory. Cílem této práce je popsat a představit takové senzory a měření provedená za účelem detekce fragmentů DNA, konkrétně látek na bázi cytosinu. Grafen je v polem řízených tranzistorech zapojen jako vodivý snímající kanál. Dopování grafenu vyvolané adsorpcí molekul na vodivém kanálu způsobuje změny transportních vlastností grafenu. Tyto změny se odrážejí v měření elektronických odezev: měření odporu grafenové vrstvy reagujícího v reálném čase na přidávání různých roztoků a závislost odporu na průběžné změně hradlového napětí. Druhou metodu měření lze provádět FET senzorem zapojeným v konfiguraci se spodním nebo elektrolytickým horním hradlem. Je sledován rozdíl mezi oběma konfiguracemi a také vliv vzdálenosti mezi grafenem a horní hradlovou elektrodou na odezvu senzoru. Výsledkem těchto měření jsou transferové křivky vykazující typické píky označující bod neutrality (Diracův bod) grafenu. Různé koncentrace roztoku analytu vedou k různým hodnotám napětí Diracova bodu, což slouží ke kvantifikaci úrovně dopování grafenu.
|
|
|
Analýza metylace DNA pomocí kapilární elektroforézy
Zahálka, Martin
This bachelor thesis, DNA methylation analysis by capillary electrophoresis, deals with the analysis of methylated DNA by capillary electrophoresis. The theoretical part introduces the general principles of methylation, asymmetric and symmetric methylation, de novo methylation and final DNA methylation. The following chapter is devoted to the methylation of DNA in bacteria, plants and animals. The possibilities of detection of methylated DNA and their characterization are also elaborated in the literature review. At the end of the theoretical part is also devoted to the chapter capillary electrophoresis. The essence of the experimental part is the separation of cytosine and methylcytosine. Capillary electrophoresis was used to analyze standard cytosine and methylcytosine solutions. During the experiment, the separation electrolyte and the separation conditions were adjusted. Ideal conditions were achieved using a 50 mM borate buffer with the addition of sodium dodecyl sulfate (SDS) with a final concentration of 60 mM, at 20 kV and 30 mBar.
|
|
|
Genomic Data Mining Techniques
Jaša, Petr ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.
|
|
|
Identifying CpG islands in genomes of eukaryotes
Urbánková, Kateřina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with searching CpG islands in DNA. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There is basic information about human and chimpanzees genome and specification of CpG islands. Practical part consists of a program that searches for CpG islands in sequences, it displayes and saves it. This work includes analysis of genes which are common for Homo sapiens, Pan troglodytes, Mus musculus and Bos taurus.
|
|
|
Alignment of DNA Parts
Pejř, Václav ; Burgetová, Ivana (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with finding the possibilities within the sphere of alignment of DNA sequences. Based on these findings, the best solution should be found with regard to the quickness of computation and quality of alignment. Following this I intend to implement and thus create a functioning program that will do the alignment. The thesis starts with introducing issues dealing with biology, DNA and genetics. The introduction is followed by a survey of algorithms that are used for alignment, their evaluation and selection of the most appropriate algorithm for the implementation. The thesis also focuses on the usage of parallel programming by means of OpenCL libraries. The alignment is being done above many sequences at the same time, so that the methods how this process can be done and how to reach the best results are being examined.
|
|
| |
guest ::
