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Full-Text Articles in Other Computer Sciences
De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian
De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of Gene Ontology …
Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang
Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang
Theses and Dissertations--Computer Science
The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We …
A Novel Computational Framework For Transcriptome Analysis With Rna-Seq Data, Yin Hu
A Novel Computational Framework For Transcriptome Analysis With Rna-Seq Data, Yin Hu
Theses and Dissertations--Computer Science
The advance of high-throughput sequencing technologies and their application on mRNA transcriptome sequencing (RNA-seq) have enabled comprehensive and unbiased profiling of the landscape of transcription in a cell. In order to address the current limitation of analyzing accuracy and scalability in transcriptome analysis, a novel computational framework has been developed on large-scale RNA-seq datasets with no dependence on transcript annotations. Directly from raw reads, a probabilistic approach is first applied to infer the best transcript fragment alignments from paired-end reads. Empowered by the identification of alternative splicing modules, this framework then performs precise and efficient differential analysis at automatically detected …