Evaluation of prediction tools and computational analysis of micro RNAs in cassava (Manihot esculentancrantz)
By: Anjana Haridas.
Contributor(s): J Sreekumar (Guide).
Material type:
BookPublisher: Vellayani Department of Plant Biotechnology, College of Agriculture 2014Description: 80p.Subject(s): Plant BiotechnologyDDC classification: 660.6 Online resources: Click here to access online Dissertation note: MSc(INT) Abstract: The study entitled “Evaluation of prediction tools and computational analysis of microRNAs in cassava (Manihot esculenta Crantz.)” was conducted at the CTCRI, Sreekariyam, Thiruvananthapuram during August 2013 to June 2014. The objectives of the study included comparison and evaluation of miRNA prediction software, computational prediction and annotation of miRNA in cassava and understanding the role of miRNA-mRNA interaction in cassava in biotic stress responses (Cassava Mosaic Virus). Experiments were also conducted to validate the presence of the predicted cassava miRNA.
The plant miRNA target prediction tools: psRNATarget and miRanda were compared for their performance. Analysis was performed to identify the optimal maximum expectation value for psRNATarget. psRNATarget with an optimum maximum expectation value of 3 was found to be a better plant miRNA target prediction tool.
Homology based method was used to identify the conserved potential cassava miRNAs. The targets for the predicted miRNA were predicted using the web tool psRNATarget and these were functionally annotated. A total of 152 miRNAs belonging to 30 miRNA families were identified having multiple targets in cassava transcripts. Majority of the microRNAs were about 21 nt in length and found in the 5’ arm of stem loop hairpin secondary structure. miRNAs had a high MFE and MFEI values. VMir Analyzer was used in the prediction of 3 Indian cassava mosaic virus miRNAs and their targets in cassava transcripts include genes involved in catalysis, regulation and stress response.
Cassava miRNA targets in cassava mosaic virus were identified using miRanda target prediction algorithm. 14 cassava miRNA families targeted Cassava Mosaic Virus with nearly perfect complementarity. Two of the cassava miRNAs having target in the viral genome was validated for their presence in healthy and CMD infected leaf sample. Primers were designed and qRT-PCR reaction was performed and their presence validated in both the samples.
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Theses
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KAU Central Library, Thrissur Theses | Reference Book | 660.6 ANJ/EV (Browse shelf) | Not For Loan | 173444 |
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MSc(INT)
The study entitled “Evaluation of prediction tools and computational analysis of microRNAs in cassava (Manihot esculenta Crantz.)” was conducted at the CTCRI, Sreekariyam, Thiruvananthapuram during August 2013 to June 2014. The objectives of the study included comparison and evaluation of miRNA prediction software, computational prediction and annotation of miRNA in cassava and understanding the role of miRNA-mRNA interaction in cassava in biotic stress responses (Cassava Mosaic Virus). Experiments were also conducted to validate the presence of the predicted cassava miRNA.
The plant miRNA target prediction tools: psRNATarget and miRanda were compared for their performance. Analysis was performed to identify the optimal maximum expectation value for psRNATarget. psRNATarget with an optimum maximum expectation value of 3 was found to be a better plant miRNA target prediction tool.
Homology based method was used to identify the conserved potential cassava miRNAs. The targets for the predicted miRNA were predicted using the web tool psRNATarget and these were functionally annotated. A total of 152 miRNAs belonging to 30 miRNA families were identified having multiple targets in cassava transcripts. Majority of the microRNAs were about 21 nt in length and found in the 5’ arm of stem loop hairpin secondary structure. miRNAs had a high MFE and MFEI values. VMir Analyzer was used in the prediction of 3 Indian cassava mosaic virus miRNAs and their targets in cassava transcripts include genes involved in catalysis, regulation and stress response.
Cassava miRNA targets in cassava mosaic virus were identified using miRanda target prediction algorithm. 14 cassava miRNA families targeted Cassava Mosaic Virus with nearly perfect complementarity. Two of the cassava miRNAs having target in the viral genome was validated for their presence in healthy and CMD infected leaf sample. Primers were designed and qRT-PCR reaction was performed and their presence validated in both the samples.
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