avsparrow.bsky.social

@avsparrow.bsky.social

8 Followers 19 Following

Genomics Scientist and Engineer; Cooking and Calisthenics Enthusiast

Using both long andshort reads we demonstrate simplified and improved alignment quality, ease of downstream analysis including identification of novel isoforms and their translational products, differential expression and more! For example, by comparing isoforms assembled from a public SIV dataset, we uncover a unique splicing donor site and junction (donor upstream of major splicing donor 0 in SIV) which is exclusively detected across most single cells in the AY69 group (CD4+ T cells from a mesenteric lymph node of SIVmac251-infected macaque). Significant differences in transcriptional landscapes are also detected with DEXSeq.
Our method consistently annotates all included major donor and acceptor sites across thousands of novel isolates. Splicing sites are strongly conserved with significant increase from the conservation of random genomic sites
Inconsistency in SD4 donor and SA7 acceptor splice site annotations in the coding sequence of the GenBank HIV-189.6 (U39362.2) annotation. The GenBank annotation (shown in red) incorrectly positions the SD4 donor site one base upstream of the canonical GT dinucleotide and the SA7 acceptor site two bases downstream of the canonical AG dinucleotide. This erroneous annotation results in the truncation of the encoded protein sequence by one complete amino acid. Our suggested corrected annotation (in orange) is shown below the GenBank annotation.
Subset of the core alternative splicing map for the HIV-1 genome illustrating the complexity of the viral transcription and how the major donor-acceptor pairs are deterministic of the protein translation.
The HIV Atlas web interface provides a simple interface for explore and download transcriptome annotations for any of the currently annotate 2,080 genomes.
Our method consistently annotates all included major donor and acceptor sites across thousands of novel isolates. Splicing sites are strongly conserved with significant increase from the conservation of random genomic sites
Inconsistency in SD4 donor and SA7 acceptor splice site annotations in the coding sequence of the GenBank HIV-189.6 (U39362.2) annotation. The GenBank annotation (shown in red) incorrectly positions the SD4 donor site one base upstream of the canonical GT dinucleotide and the SA7 acceptor site two bases downstream of the canonical AG dinucleotide. This erroneous annotation results in the truncation of the encoded protein sequence by one complete amino acid. Our suggested corrected annotation (in orange) is shown below the GenBank annotation.
Subset of the core alternative splicing map for the HIV-1 genome illustrating the complexity of the viral transcription and how the major donor-acceptor pairs are deterministic of the protein translation.