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Currently implemented alignment methods are Mosaik and BWA.
The framework can be extended to implement new alignment and classification algorithms.
This is the reason why several of them are deciding to implement optical alignment systems to monitor the displacement of tracking elements in operation.
Strapdown inertial navigation system cannot easily implement initial alignment on moving base if without the prior "one shot" transfer from another master inertial navigation system and strict constraints on moving trajectory, because the initial coarse attitude cannot be effectively achieved.
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.
A complete set of files needed to implement this alignment pipeline is provided at https://github.com/justin-lack/Drosophila-Genome-Nexus.git, along with a step-by-step list of commands, which is also provided here as Supporting Information, File S1.
(d-f) Same cross-sections shown as (a-c) resulting from implementing our alignment method.
We implemented an alignment approach that takes these nucleotide misincorporation patterns into account (SOM Text 3) and aligned the Neandertal sequences to either the reference human genome (UCSC hg18), the reference chimpanzee genome (panTro2), or the inferred human-chimpanzee common ancestral sequence (SOM Text 3).
Then the implemented multiple alignment function for distinct clades was used to find conserved protein sequences of the selected candidates (Table S1).
BWA employs roughly the same idea but it implements gapped alignment.
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).
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