In choosing the methods for our study, we only considered the availability of software and the simplicity of implementing the alignment scoring functions (see the Results section).
HPG-Methyl implements the alignment strategy described in Section 2. However, in order to take advantage of the parallel architectures available in current computers, it follows a very similar parallel pipeline to the one used by HPG-Aligner (Martínez et al., 2013; Tárraga et al., 2014), but adapted to the specific features of methylation analysis.
We chose to demonstrate examples for AGE, CrossMatch (http://www.phrap.org/phredphrapconsed.html, implementing the Smith Waterman alignment), GAP3 (Huang and Chao, 2003) (implementing a generalized global alignment with piecewise gap penalty), and Blat (Kent, 2002), a popular heuristic alignment program aimed at aligning highly similar sequences with large gaps.
To avoid such massive effort, merlin was used to implement the remote similarity alignments between the user set of genes (or full genome as was the case) and the previously selected remote NCBI database, as well as retrieve and classify each homologue's annotation, providing comprehensible information.
We implemented the delay alignment and phase rotation modules on a Texas Instruments C6678 DSP with 8 cores.
In this study, two methods are implemented: the sequence alignment method based on the BLASTP and the feature selection method with amino acid composition and pseudo amino acid composition features [90].
An R-package implementing the graph alignment is available from the bioconductor website [ 36].
Rip sequences were aligned using the ProGraphMSA program, which implements the evolution-aware alignment [ 65, 66].
Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve.wisc.edu/mauve
In order to facilitate sequence homology searches, we implemented the basic local alignment search tool (BLAST) (21).
