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ANTICALIgN: visualizing, editing and analyzing combined nucleotide and amino acid sequence alignments for
Alexander Jarasch1, Melanie Kopp1, Evelyn Eggenstein1
1Munich Center for integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, Freising (Weihenstephan) 85354, Germany.
Protein Engineering, Design & Selection : PEDS
|June 5, 2016
Summary
ANTIC ALIGN is new software for visualizing and analyzing DNA/protein sequences in protein engineering. It uniquely displays nucleotide and amino acid sequences simultaneously, aiding in protein design and evolution.
Area of Science:
- Bioinformatics
- Protein Engineering
- Computational Biology
Background:
- Combinatorial protein engineering requires simultaneous analysis of nucleotide and amino acid sequences.
- Existing tools often lack integrated visualization for both DNA and protein sequences.
- Efficient analysis of sequence alignments is crucial for protein design and selection.
Purpose of the Study:
- To introduce ANTIC ALIGN, an interactive software for simultaneous visualization, analysis, and modification of DNA and protein sequence alignments.
- To provide unique features for protein engineering, including simultaneous display of nucleotide and translated amino acid sequences.
- To facilitate the analysis of sequences arising from combinatorial protein engineering, design, and selection.
Main Methods:
- Template-based multiple sequence alignment (MSA) using unmutated protein as reference.
- Conventional global alignment for evolutionary related sequences.
- Similarity-based clustering algorithms for identifying duplicates and conserved features.
- Automatic translation of nucleotide sequences to amino acid sequences with options for reading frame selection and feature highlighting.
Main Results:
- ANTIC ALIGN enables simultaneous visualization and manipulation of nucleotide and amino acid sequences.
- The software supports template-based and global alignment strategies.
- Clustering algorithms aid in identifying sequence features and duplicates.
- Features like hiding conserved residues simplify analysis of mutated positions.
- The tool handles non-standard genetic code elements like suppressed stop codons and non-natural amino acids.
Conclusions:
- ANTIC ALIGN is a powerful tool for protein engineering, particularly for analyzing sequences from combinatorial approaches.
- It offers unique advantages by integrating DNA and protein sequence analysis.
- The software is applicable to antibody engineering and directed enzyme evolution.
- Demonstrated utility in selecting Anticalins against tumor vasculature markers.
