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Project Settings
Robert J. Gifford edited this page Nov 30, 2024
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Project settings tailor the analysis and handling of sequence data within GLUE projects by defining how sequences are processed, translated, and normalized.
The HBV-GLUE project settings are defined in this project build file, and are as follows:
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Setting:
ignore-nt-sequence-hyphens=true -
Description: This setting ensures that any hyphens (
-) in nucleotide sequences are ignored during processing. Hyphens, often representing alignment gaps, do not interfere with analyses such as translation or sequence comparisons.
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Setting:
translate-beyond-possible-stop=true -
Description: Enables translation of nucleotide sequences past ambiguous codons (e.g.,
NNN) that might represent a possible stop codon. This setting is useful for sequences with uncertain or incomplete data, ensuring continuity in protein translations.
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Setting:
translate-beyond-definite-stop=true - Description: Allows translation of nucleotide sequences beyond known stop codons. This feature is essential for exploring downstream open reading frames (ORFs) and non-standard translation scenarios.
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Setting:
sequence-reverse-complement-boolean-field=reverse_complement -
Description: Specifies a custom boolean field (
reverse_complement) in the sequence table to track whether sequences should be reverse-complemented during processing. This ensures accurate handling of sequence orientation, particularly for viral genomes with reverse-strand transcription.
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Setting:
sequence-rotation-integer-field=rotation -
Description: Defines a custom integer field (
rotation) used to apply rotation transformations to circular HBV genomes. This normalizes sequence positions, aligning them to a defined reference point for consistent analysis.
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Setting:
project-version=0.1.11 - Description: Identifies the version of the HBV-GLUE core project.