GencoDymo2 - Comprehensive Analysis of 'GENCODE' Annotations and Splice Site
Motifs
A comprehensive suite of helper functions designed to
facilitate the analysis of genomic annotations from the
'GENCODE' database <https://www.gencodegenes.org/>, supporting
both human and mouse genomes. This toolkit enables users to
extract, filter, and analyze a wide range of annotation
features including genes, transcripts, exons, and introns
across different 'GENCODE' releases. It provides functionality
for cross-version comparisons, allowing researchers to
systematically track annotation updates, structural changes,
and feature-level differences between releases. In addition,
the package can generate high-quality FASTA files containing
donor and acceptor splice site motifs, which are formatted for
direct input into the 'MaxEntScan' tool (Yeo and Burge, 2004
<doi:10.1089/1066527041410418>), enabling accurate calculation
of splice site strength scores.
