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What are the limitations of dynamic programming for sequence alignment?

Structural alignment

Smith–Waterman algorithm

Multiple sequence alignment

Alignment-free sequence analysis

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Dynamic programming for sequence alignment has several limitations. One limitation is the high computational complexity, especially when dealing with large datasets such as DNA sequences . Another limitation is the difficulty in handling insertions and deletions, which are common errors in sequencing technologies . Additionally, there are mathematical mistakes in some implementations of dynamic programming algorithms, leading to sub-optimal alignments . These mistakes can have a detrimental impact on downstream analyses in bioinformatics . Another limitation is the need for additional calculations and analysis when dealing with wild card positions in sequences . Overall, these limitations highlight the challenges and potential errors associated with using dynamic programming for sequence alignment.

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Journal Article•DOI Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming Axel Fürstberger, Markus Maucher, Hans A. Kestler - Show less +2 more 02 Jan 2015-Journal of Statistical Computation and Simulation 5 Citations	The limitations of dynamic programming for sequence alignment are not mentioned in the provided paper.
Patent Implementation of dynamic programming in multiple sequence alignment Bhatnagar Amogh, Bhatnagar Anidhya - Show less +1 more 08 Aug 2019	The limitations of dynamic programming for sequence alignment are not mentioned in the provided paper.
Open access•Posted Content•DOI Are all global alignment algorithms and implementations correct Tomas Flouri, Kassian Kobert, Torbjørn Rognes, Alexandros Stamatakis - Show less +3 more 12 Nov 2015-bioRxiv 5 Citations	The limitations of dynamic programming for sequence alignment are not mentioned in the provided paper.
Open access•Journal Article•DOI A short note on dynamic programming in a band. Jean-François Gibrat 15 Jun 2018-BMC Bioinformatics 3 Citations	The limitations of dynamic programming for sequence alignment are not mentioned in the provided paper.
Book Chapter•DOI DNA Sequence Alignment Using Dynamic Programming Niharika Singh, Gaurav Rajput, Yash Dixit, Aastha Sehgal - Show less +3 more 07 Jun 2019	The limitations of dynamic programming for sequence alignment are not mentioned in the provided paper.

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