Project Settings - giffordlabcvr/Hepadnaviridae-GLUE GitHub Wiki

Project settings tailor the analysis and handling of sequence data within GLUE projects by defining how sequences are processed, translated, and normalized.

The Hepadnavirus-GLUE project settings are defined in this project build file, and are as follows:

1. Ignore Nucleotide Sequence Hyphens

• 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.

2. Translate Beyond Possible Stop Codons

• 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.

3. Translate Beyond Definite Stop Codons

• 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.

4. Sequence Reverse Complement Tracking

• 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.

5. Sequence Rotation Normalization

• 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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