Please note that the content of this book primarily consists of articles available from Wikipedia or other free sources online. In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or Protein to identify regions of similarity that may be a consequence of ...
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Word-based alignment-free algorithms come in different colors and flavors, with methodological variations at each of the three basic steps. In the first step, one can try any resolutions of word lengths—it is important to choose words that are not likely to commonly appear in a sequence (the...
Alignment-free approaches to sequence comparison can be defined as any method of quantifying sequence similar- ity/dissimilarity that does not use or produce alignment (assignment of residue–residue correspondence) at any step of algorithm application. From the start, such restric- tion places the ...
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 ...
In this study, we estimated the parameters of Markov chain by considering the frequencies of occurrence of the all possible amino acid pairs from each alignment-free protein sequence. These estimated Markov chain parameters were used to calculate similarity between two protein sequences based on a ...
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
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 ...