The authors used a custom Haskell embedding of algebraic DP to implement the alignment algorithm for rapid prototyping, easy evaluation of the scoring function and optimizations.
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.
An R-package implementing the graph alignment is available from the bioconductor website [ 36].
Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve.wisc.edu/mauve
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].
We also employed "Multiple Alignment Using Fast Fourier Transform" (Katoh and Kuma 2002) as an alternative method of alignment, but found no difference in our findings from implementing the "classic" methods of alignment (data not shown).
Genome sequences were aligned using the MAFFT program [ 49, 50] implementing the FFT-NS-1 alignment strategy.
To determine the extent of sequence similarity, alignments between predicted proteins and best BLAST-hit sequences were performed using NEEDLE software implementing the Needleman-Wunsch global alignment algorithm and using the BLOSUM62 matrix [ 58].
