TranslatorX

TranslatorX aligns protein-coding nucleotide sequences by leveraging their amino acid translations to produce codon-aware nucleotide alignments for comparative and evolutionary analyses.

Key Features:

• Utilization of Genetic Codes: Supports all documented genetic codes and allows assigning different genetic codes for each sequence.
• Multiple Alignment Programs: Incorporates a variety of multiple alignment programs to perform amino-acid-level alignments.
• Handling Ambiguous Codons: Translates ambiguous codons when possible to preserve information during translation-based alignment.
• Alignment Cleaning with GBlocks: Cleans nucleotide alignments using GBlocks based on protein information to remove poorly aligned regions.
• Comprehensive Output Options: Produces Jalview graphical visualizations, codon-based alignments colored by corresponding amino acids, measures of compositional bias, and first-, second-, and third-codon-position-specific alignments.

Scientific Applications:

• Evolutionary studies: Generates codon-aware alignments that use amino-acid conservation to improve detection of conserved regions for evolutionary analyses.
• Functional genomics: Provides codon-position-specific alignments and compositional bias measures useful for functional and coding-sequence analyses.
• Homology-based analyses: Produces nucleotide alignments that reflect protein-level homology to support inference of biological homology.

Methodology:

Translate nucleotide sequences using specified genetic codes (per-sequence assignment allowed), translate ambiguous codons when possible, perform amino-acid alignments with multiple alignment programs, clean nucleotide alignments with GBlocks using protein information, and generate codon-based alignments, codon-position-specific alignments, compositional bias measures, and Jalview visualizations.