| Summary: | 碩士 === 東海大學 === 生命科學系 === 100 === 外文摘要
Metagenomics is a discipline that studies environmental microbes. Sequence-based methods are widely adopted in metagenomics. In sequence-based metagenomics, genomes are extracted from environmental samples and DNA fragments are then sequenced. The sequenced DNA fragments (reads) are subjected to be further assembled to generate contigs for further analyzing or they can be directly analyzed by gene-centric methods, in which functional genes are annotated of reads and species diversity postulated. Blastx is a tool widely adopted in gene-centric analyzed. However, its sensitivity and specificity are usually low and most of researchers are not fully aware of the drawbacks. Therefore, we address several questions to check potential parameters that affect the performance of blastx. To mimic sequence-based metagenomic studies, we used Escherichia coli BL21-Gold(DE3)pLysS AG genome and simulated high-throughput sequencing in silico followed by blastx analysis. We first tested whether sequence lengths affect blastx performance. Second, we tested whether e-value affect blastx performance. Third, we checked whether the gene density is a critical factor to affect blastx performance. Recent results showed that sequence lengths, e-values and gene densities are important factors to affect the sensitivity and the specificity of blastx.
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