Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generati...
Alignment-free approaches to sequence comparison can be defined as any method of quantifying sequence similarity/dissimilarity that does not use or produce alignment (assignment of residue–residue correspondence) at any step of algorithm application. From the start, such restriction places the alignment-...
Rapid methods for alignment-free sequence comparison make large-scale comparisons between sequences increasingly feasible. Here we study the power of the statistic D2, which counts the number of matching k-tuples between two sequences, as well as D2*, which uses centralized counts, and D2S, ...
et al. (2013) Alignment-free genetic sequence compari- sons: a review of recent approaches by word analysis. Brief. Bioinformatics, 15, 890-905.Bonham-Carter,O. et al. (2013) Alignment-free genetic sequence comparisons: A review of recent approaches by word analysis. Brief. Bioinform., 15...
We built an alignment-free phylogenetic tree, employing the algorithmic information distance between each pair of sequences to construct the distance-matrix. The tree represents the history of the set of molecular sequences, and allows us to follow in more detail how chemical function improves with...
We also trained an MSA-free version of AlphaFold2, denoted by AlphaFold2-Single, by only using the single sequences as input. To evaluate the accuracy of HelixFold-Single and other methods, we utilized a commonly used metric, that is, the template modelling score (TM-score)18. Figure 2 ...
A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence
Alignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes of deducing “nearby” species in a reference
DNA sequence assembly, sequence alignment, contig editing, and mutation detection software for Windows and Mac OS X. View & edit sequence assemblies.
The resulting sequence alignments are assessed using two different tests: First, we assess the alignment quality by measuring the derived structural similarity for cases in which structures are available. In a second test, we quantify the ability of the significance score of the alignments to ...