UCSC genome browser uses binning strategy to retrieve genes more efficiently than simply creating a B-tree on the start and end coordinates. This certainly serves the purpose well because query ranges is not a strengthen of B-tree. But binning + B-tree basically provides a crude approximation to R-tree (using spatial index) that has already been implemented in MySQL. I'm wondering why is this spatial index not used in the first place? Is it because the spatial index is a relatively new feature that was not implemented in MySQL when the UCSC GB was developed? Just curious.
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by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
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05-06-2024, 07:48 AM -
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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
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04-22-2024, 07:01 AM -
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