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Transcription motif finding in non-model organisms
Helešicová, Klára ; Jurečková, Kateřina (referee) ; Musilová, Jana (advisor)
This bachelor thesis deals with the search for DNA motifs in non-model organisms. The first part explains the process of transcription, the concept of mutual information and an algorithm using mutual information. The second part describes the distribution of motif searching methods and examples of algorithms. The third part contains an overview of transcription motif databases. The practical part contains a description of the creation of a dataset for a non-model organism, a description of the proposed algorithm and its testing on the dataset. Then, the results of the proposed algorithm were compared with the results of FIRE and MEME algorithms.
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Transcription motif finding in non-model organisms
Helešicová, Klára ; Jurečková, Kateřina (referee) ; Musilová, Jana (advisor)
This bachelor thesis deals with the search for DNA motifs in non-model organisms. The first part explains the process of transcription, the concept of mutual information and an algorithm using mutual information. The second part describes the distribution of motif searching methods and examples of algorithms. The third part contains an overview of transcription motif databases. The practical part contains a description of the creation of a dataset for a non-model organism, a description of the proposed algorithm and its testing on the dataset. Then, the results of the proposed algorithm were compared with the results of FIRE and MEME algorithms.
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De novo transcriptomics and its use in non-model organisms
Čalounová, Tereza ; Pluskal, Tomáš (advisor) ; Svatoňová, Petra (referee)
The rise of second generation sequencing enabled the study of non-model organisms. Without the requirement of having a reference genome, de novo transcriptomics allows the study of functional elements of their genomes. That way, the great complexity of non-model organisms can be explored. This thesis gives a comprehensive overview of the de novo transcriptomics experiment workflow from a bioinformatics perspective. The emphasis was placed on both theoretical background and practical approaches. This work also highlights new methods in de novo transcriptomics which may start to dominate in the near future. The practical part of the work presents transXpress - a de novo transcriptome assembly and annotation pipeline. Its use is demonstrated on a non-model plant long pepper (Piper longum) with medicinal potential. Keywords: transcriptomics, de novo transcriptomics, transcriptome, RNA-Seq, non-model organism, assembly
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