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Aligning coding sequences with frameshift extension penalties.

Safa Jammali1, Esaie Kuitche1, Ayoub Rachati1

  • 1Département d'informatique, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC J1K2R1 Canada.

Algorithms for Molecular Biology : AMB
|April 5, 2017
PubMed
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This study introduces a novel algorithm for aligning coding DNA sequences (CDS) that accurately accounts for frameshift translation initiation and length. The new method improves upon existing approaches by considering both nucleotide and amino acid levels, offering robust performance in gene evolution studies.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics
  • Molecular Evolution

Background:

  • Frameshift translation generates novel coding DNA sequences (CDS) and functions, crucial for gene evolution.
  • Existing algorithms for CDS alignment either ignore frameshifts or only consider their initiation, not their length.
  • Accurate CDS alignment is essential for understanding genetic variation and evolutionary processes.

Purpose of the Study:

  • To develop a novel algorithm for pairwise coding DNA sequence (CDS) alignment that incorporates frameshift translation initiation and length.
  • To simultaneously consider both nucleotide and amino acid sequences for more accurate CDS comparison.
  • To provide a robust and versatile tool for analyzing gene evolution and identifying functional variations.
Keywords:
Coding DNA sequences pairwise alignmentDynamic programmingFrameshifts

Related Experiment Videos

Main Methods:

  • Introduction of a new scoring scheme with a penalty cost for frameshift extension length.
  • Development of an algorithm that considers the full search space of feasible CDS alignments.
  • Simultaneous analysis of nucleotide and amino acid sequences, unlike previous methods.

Main Results:

  • The new algorithm effectively accounts for both frameshift initiation and length in CDS alignment.
  • The scoring scheme provides an adequate similarity score by penalizing frameshift extension length.
  • The algorithm achieves the same asymptotic time complexity as the classical Needleman-Wunsch algorithm.

Conclusions:

  • The developed method demonstrates robustness to parameter changes compared to existing CDS alignment techniques.
  • It performs well in both the presence and absence of frameshift translations, offering a balanced approach.
  • The implementation is publicly available, facilitating its application in comparative genomics and evolutionary studies.