- Oct 01, 2024
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Studer Gabriel authored
SCHWED-6400
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- Jun 21, 2024
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Studer Gabriel authored
Must be enabled at compile time. It bends around the respective naive implementations in OST to their parasail counterpart. On one hand its faster and on the other hand it should fix potential suboptimal alignments which are reported in SCHWED-6266
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- Jun 12, 2024
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Studer Gabriel authored
Parasail: https://github.com/jeffdaily/parasail It's faster than the pairwise sequence algorithms we have in OpenStructure. However, the main reason to check out another solution is the fact that OpenStructure may return suboptimal alignment results. This is a result of how the dynamic programming table is built. If for a certain cell in the dynamic programming table a match state and insertion state score equally, match is preferred. There is a chance that we would get a better score later on if we would stick with the insertion state (gap open penalties vs. gap extension penalties). Not sure if this will be fixed in the near future.
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