ArticleBMC genomics2017
MARS: improving multiple circular sequence alignment using refined sequences.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
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- Telomere-to-telomere genome assembly of the Dipteran Bactrocera dorsalis from a single individual.Nature communications · 2025Article
- A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA.Molecular ecology resources · 2025Article
- Genomic Architecture of the Clownfish Hybrid Amphiprion leucokranos.Genome biology and evolution · 2025Article
- Prediction of Circular RNA Secondary Structures and Their Targets.Advances in experimental medicine and biology · 2025Review
- Viroid-like colonists of human microbiomes.Cell · 2024Article
- Rapid speciation in the holopelagic ctenophorebioRxiv : the preprint server for biology · 2024Article
- Full-genome sequencing of dozens of new DNA viruses found in Spanish bat feces.Microbiology spectrum · 2024Article
- Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria.Nature communications · 2024Article
- Viroid-like colonists of human microbiomes.bioRxiv : the preprint server for biology · 2024Article
- DNA barcodes are ineffective for species identification ofBiodiversity data journal · 2024Article
- An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.PloS one · 2024Article
- Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels.ISME communications · 2023Article
- Rotate: A command-line program to rotate circular DNA sequences to start at a given position or string.Wellcome open research · 2023Article
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2 authors.
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Abstract
backgroundA fundamental assumption of all widely-used multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a sequence starts or ends can be totally arbitrary due to a number of reasons: arbitrariness in the linearisation (sequencing) of a circular molecular structure; or inconsistencies introduced into sequence databases due to different linearisation standards. These scenarios are relevant, for instance, in the process of multiple sequence alignment of mitochondrial DNA, viroid, viral or other genomes, which have a circular molecular structure. A solution for these inconsistencies would be to identify a suitable rotation (cyclic shift) for each sequence; these refined sequences may in turn lead to improved multiple sequence alignments using the preferred multiple sequence alignment program.
resultsWe present MARS, a new heuristic method for improving Multiple circular sequence Alignment using Refined Sequences. MARS was implemented in the C++ programming language as a program to compute the rotations (cyclic shifts) required to best align a set of input sequences. Experimental results, using real and synthetic data, show that MARS improves the alignments, with respect to standard genetic measures and the inferred maximum-likelihood-based phylogenies, and outperforms state-of-the-art methods both in terms of accuracy and efficiency. Our results show, among others, that the average pairwise distance in the multiple sequence alignment of a dataset of widely-studied mitochondrial DNA sequences is reduced by around 5% when MARS is applied before a multiple sequence alignment is performed.
conclusionsAnalysing multiple sequences simultaneously is fundamental in biological research and multiple sequence alignment has been found to be a popular method for this task. Conventional alignment techniques cannot be used effectively when the position where sequences start is arbitrary. We present here a method, which can be used in conjunction with any multiple sequence alignment program, to address this problem effectively and efficiently.
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