What is it about?

Applicable for a more accurate detection of continuous insertion/deletions (indels) in genes’ fragments, associated with disorders caused by over-repetition of a certain codon. The improvement comes from the tendency to pinpoint indels in the least preserved nucleotide pairs. All nucleotide pairs that occur less frequently are classified as less preserved and they are considered as mutated codons whose mid-nucleotides were deleted.

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Why is it important?

FUNDAMENTAL PROPERTIES: 1. Dinucleotide frequencies are computed and considered when pinpointing indels in genes. 2. When aligning genes, Indels are allocated in the middle of the least preserved dinucleotides, as they are supposed to be mutated codons whose mid-nucleotides were deleted. 3. Property number 2. makes the algorithm suitable for accurate detection of Huntington's disease and other diseases, which are associated with excessive trinucleotide repetitions, such as: Spinocerebellar ataxia and Dentatorubropallidoluysian atrophy. COMPUTATIONAL IMPROVEMENTS: 1. Does not depend on any specific metrics. 2. Provides maximum number of matching nucleotides per local alignment. 3. Does not reject any consistent, common match, as may be the case with Smith-Waterman.


Four crucial aspects outline the benefit of the algorithm. 1. First, the algorithm allows precise detection of missing glutamine-coding triplets in polyglutamine tracts of partial cds of huntingtin gene, due to its predisposition to pinpoint indels in less frequently occurring nucleotide pairs. 2. Runs faster than Smith–Waterman for very similar DNA, but not at the cost of generating partial or shortened alignments. 3. Requires less memory than the most memory efficient dynamic programming algorithm, the Huang's algorithm. 4. Unlike Smith–Waterman, the algorithm does not reject any of the matching regions/nucleotides which can be included in the final alignment.

Ph.D Done Stojanov
Univerzitet Goce Delcev Stip

Read the Original

This page is a summary of: TMO: time and memory optimized algorithm applicable for more accurate alignment of trinucleotide repeat disorders associated genes, Biotechnology & Biotechnological Equipment, February 2016, Taylor & Francis,
DOI: 10.1080/13102818.2015.1114428.
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