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Sigma uses a third-party short-read alignment algorithm to align all metagenomic reads onto every reference genome.
Despite that, our method (like many other genome aligners) applies a global alignment algorithm to all inter-anchor segments, navely assuming that homology exists.
Subsequently, these sequences were aligned using a global alignment algorithm to remove sequences for which the best blast hit represented only local homology.
For cruzain, PDB entries 1aim, 1me4 and 1me3 were aligned with falcipain 2 using Modeller's structure based alignment algorithm to serve as templates for the complex.
Then, they used robust alignment algorithm to choose the best subset of matched points against incorrect matches and multiple matches.
Some ICP-based approaches have an initial guess or a coarse alignment algorithm to speed up the ICP algorithm.
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This allows binding sites to relocate within the regulatory sequence, making it difficult for alignment algorithms to correctly align them.
However, the main objective of their work was to use sequence alignment algorithms to produce one robust (i.e., typo-free) lyric for a given song.
While there are optimal alignment algorithms to compute pairwise homology, their deployment for large-scale is currently not feasible; instead, heuristic methods are used at the expense of quality.
A reason for the absence of any evolutionary conserved interactions may also be based on limitations of sequence alignment algorithms to accurately detect homologies between eukaryotic and Plasmodium specific proteins.
We were unable to identify a common sequence motif using standard tools (e.g., MEME, [ 30]) and are currently attempting to combine structure alignment algorithms to this end.
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