Software and databases

Sequence Retrieval
  • NCBI & UniProt — protein sequence databases used to retrieve genomic and thermophilic sequences
Clustering
  • CD-HIT — clusters sequences by similarity to reduce redundancy
Alignment
  • MAFFT — multiple sequence alignment tool
Trimming
  • trimAl — removes poorly aligned regions from the MSA
Structure & Solvent Accessibility
  • FreeSASA — calculates solvent accessible surface area
  • ChimeraX — molecular visualization and structure analysis
Conservation Analysis
  • goalign — MSA manipulation and PSSM extraction

Statistical analysis - Python

Custom Python scripts were used for the statistical analyses and the KL divergence.

The packages used were:

  • NumPy — numerical array operations and matrix handling
  • pandas — tabular data loading and manipulation
  • SciPy — statistical tests (Chi-square, Fisher’s exact, Mann-Whitney U, T-test, KL divergence)