In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described.
Unlike a pure sequence-based classification, the pure structure-based classification leads to a directly useful application (structural alignment) and often easily interpretable results.
We evaluated multiple aligners based on criteria, including application-specific alignment feature, computational efficiency, and alignment accuracy.
We further used long-read and short-read datasets from both real-life and in silico NGS data for comparative analysis and evaluation of these aligners focusing on three criteria, namely, application-specific alignment feature, computational performance, and alignment accuracy.
Experimental evaluation and results are presented in Section 3. Section 4 presents two applications: automatic alignment of audio and lyrics in polyphonic music and a small-scale query-by-singing application.
For biological applications, sequence alignment is an important strategy to analyze DNA and protein sequences.
The assembly of MEMS-based devines in certain applications requires alignment within tolerances better than ±1μm.
Recent measurements performed at the beamline include non-destructive depth dependent variable kinetic energy measurements of dielectric and semiconductor films and interfaces for microelectronics applications, band alignment at buried interfaces, and the electronic structure of bulk-like materials.
Phylogeny reconstruction is an important application of alignment-free sequence comparison.
Using VCM language in medical applications requires alignment with medical reference terminologies.
The application-specific alignment features were considered as follows: multithread, gapped alignment analysis, paired-end alignment analysis, trimming alignment analysis, and bisulfite alignment analysis.
