Standard Operational Procedures: Gene Model and Functional Curation |
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The following is completed documentation of many of JCVI's standard operating procedures (SOPs)
for gene model and functional curation. Each SOP outlines the purpose and scope of each process or procedure, all requirements necessary
to carry out each procedure, a detailed description of the process or analysis, and all measures utilized to ensure that data and data
types generated are consistent, current, and maintain specific quality requirements.
- Gene Model Curation
- Homology Searches
- Outlines all of our pre-computed homology searches run to generate evidence
for functional annotation.
- Functional Curation
- Functional Automated Annotation
Defines our automated annotation program that generates putative functional annotation to each gene model.
- Functional Manual Curation
Documents the layered evidence based approach used by curators for accurately assigning descriptive functional annotation to each gene
model.
- Start Site Curation
Describes the criteria used by curators when evaluating and editing the initiation codon for each gene model.
- Frameshift Edit and Analysis
Describes the procedure used by curators for evaluating and editing potential frame shifts, point mutations, and sequence ambiguities.
- Overlap Analysis and Curation
Defines the criteria used by curators when reviewing overlapping regions of gene models.
- Supporting Documentation
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