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GlimmerHMM
Kind of a beginner question here which is not specific to any particular organism. To train GlimmerHMM you need a file with the genes, and a file with the coordinates of the exons within those genes. The genes are downloadable from NCBI, but I am wondering how you get the exon coordinates. Are they also downloadable from NCBI? I feel like they should be, otherwise they wouldn't have the genes available if they didn't have some idea of the intron-exon boundaries within the genes. Or is the availability of the exon information dependent on the degree of annotation of the organism?
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM