Applications of alignment-free approaches include protein classification [ 2- 5], read alignment [ 6- 8], isoform quantification from RNAseq reads [ 9], sequence assembly [ 10], read-binning in metagenomics [ 11- 16] or analysis of regulatory elements [ 17- 20].
To summarize, it was clear that Novoalign and Segemehl beneficially supported wide applications of multiple alignment features analysis, namely, gapped alignment, paired-end alignment, and bisulfite alignment.
Phylogeny reconstruction is an important application of alignment-free sequence comparison.
The application of alignment-free supervised classification methods on metagenome data has not been well explored yet.
The application of alignment-free methods in large-scale phylogenomics is currently limited, and the scalability and robustness of these methods remain to be systematically investigated.
In addition to the previously demonstrated applications of sequence alignment, fold identification, template selection, and homology modeling, we demonstrate herein, application of the described PCAIN-based structure prediction methodology to derive biological insight into potential structure-function relationships of proteins with hitherto unresolved structure.
Other applications of sequence alignment require different algorithms.
In addition, the flexible nature of this algorithm makes it suitable for different applications of network alignment.
In many applications of PPIN alignment, the underlying objective is to equivalence proteins with related function and interacting partners.
One of the applications of network alignment is to use the available information on the protein complex in one species to predict the protein complex components in another species.
