MARS: improving multiple circular sequence alignment using refined sequences

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.

The roles of hybridization and habitat fragmentation in the evolution of Brazil’s enigmatic longwing butterflies, Heliconius nattereri and H. hermathena

“…We used NOVOplasty to extract and assemble mtDNA reads from these accessions using bait sequences indicated in Table S3, a kmer size of 39, and an expected size range of 12-22 kb [43]. We aligned all mtDNA genomes using the multiple circular sequence alignment program MARS [87]. Finally, we inferred the mtDNA phylogeny using IQtree v1.6.12 using the best-fit model determined using Mod-elTest and estimated support using 1000 ultrafast bootstraps [42,88,89].…”

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram‐staining properties

“…Upon assembly it became clear that the predicted V. parvula prophage 1 was truncated and so the prediction was extended to include the full prophage sequence. Sequences were rotated with MARS (Ayad and Pissis, ) to ensure that the sequences started and ended at the same point (as the genomes are circular), and global alignment was performed with emboss stretcher (Rice et al ., ) with gapopen 16 and gapextend 4 penalties. Percent matches between the sequences was then calculated and genome maps visualized.…”

Selfing is the safest sex forCaenorhabditis tropicalis

“…After circular polishing with long-reads (Unicycler), sequences were 14394 and 14027 bp. We rotated these with five copies of the C. elegans mitochondrial genomes to optimise linear homology using MARS (Ayad & Pissis, 2017) .…”