Figure 9 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
The Gene Model Checker checklist indicated the presence of in-frame stop codons within coding exons 2, 3, 4, 5, 7, and 8 of the proposed gene model for chico-PB in D. eugracilis. The checklist also reports the use of a non-canonical GG splice donor site for CDS 1, and that the total length of the coding region (2,807 nt) is not divisible by three. To address these errors, the annotator should verify the annotation for the item associated with the first error in the checklist (i.e., the end coordinate for the first coding exon and its corresponding splice donor site). In this example, the end of the first coding exon should be changed from 4,678,301 to 4,678,302 based on the available evidence on the GEP UCSC Genome Browser. This change will resolve the remaining failures in the checklist.
Source publication
Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/ ) developed a stru...
Context in source publication
Context 1
... failures in the Gene Model Checker checklist (as shown in Figure 9) are typically caused by the selection of incompatible splice sites during the "Refine coding exon coordinates" stage of the analysis. Most of these errors can be resolved by scrutiny of the coordinates for the checklist item where the first error is reported by the Gene Model Checker. ...
Citations
... Molecular structure visualization is gaining popularity in chemistry (Tsaparlis, 1997;Jones, 2013) and biology education (Terrell and Listenberger, 2017). Similarly, the use of bioinformatics tools is growing in biology education (Ditty et al., 2010;Rele et al., 2023). MCSs provide an excellent platform for teaching students how to synthesize information from 3D structural and bioinformatics data with their knowledge of chemistry (e.g., the chemical interactions within and between biomolecules) and biology (e.g., information storage, signal transduction, metabolism), to gain a deeper understanding of the case-related research question(s). ...
Molecular case studies (MCSs) provide educational opportunities to explore biomolecular structure and function using data from public bioinformatics resources. The conceptual basis for the design of MCSs has yet to be fully discussed in the literature, so we present molecular storytelling as a conceptual framework for teaching with case studies. Whether the case study aims to understand the biology of a specific disease and design its treatments or track the evolution of a biosynthetic pathway, vast amounts of structural and functional data, freely available in public bioinformatics resources, can facilitate rich explorations in atomic detail. To help biology and chemistry educators use these resources for instruction, a community of scholars collaborated to create the Molecular CaseNet. This community uses storytelling to explore biomolecular structure and function while teaching biology and chemistry. In this article, we define the structure of an MCS and present an example. Then, we articulate the evolution of a conceptual framework for developing and using MCSs. Finally, we related our framework to the development of technological, pedagogical, and content knowledge (TPCK) for educators in the Molecular CaseNet. The report conceptualizes an interdisciplinary framework for teaching about the molecular world and informs lesson design and education research.
