tbg-tools

tbg-tools predicts the effects of single-nucleotide polymorphisms (SNPs) on protein-coding genes by storing per-gene nucleotide data in the tab-separated tbg file format to enable amino-acid-level consequence analysis.

Key Features:

• tbg file format: A tab-separated file format that stores comprehensive nucleotide data for each gene to support variant consequence prediction.
• SNP impact analysis: Predicts whether nucleotide variants cause amino acid changes in protein-coding genes and reports the resulting amino acid composition alterations.
• Scaffold position lookup: Provides lookup of positions on scaffolds and returns detailed nucleotide and variant information for those positions.
• Automation capabilities: Supports automation of analytical processes for handling genome-wide genetic variation datasets.
• Implementation: Implemented in Python.

Scientific Applications:

• Genomics: Annotates coding-region variants by predicting amino-acid-level consequences of SNPs across genomes.
• Evolutionary biology: Assesses potential functional effects of nucleotide substitutions on proteins for evolutionary inference.
• Personalized medicine: Aids interpretation of coding variants that may affect protein function in clinical or translational contexts.
• Functional genomics: Enables investigation of the functional implications of genetic variation on protein sequences.

Methodology:

Store comprehensive nucleotide information in the tbg tab-separated file format and analyze nucleotide variants to predict changes at the amino-acid level; supports automated analysis and scaffold position queries for genome-wide variation data.