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Add secondary palmprint detection routine #7

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ababaian opened this issue Nov 9, 2021 · 0 comments
Open

Add secondary palmprint detection routine #7

ababaian opened this issue Nov 9, 2021 · 0 comments

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@ababaian
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ababaian commented Nov 9, 2021

There appears to be an issue with detecting palmprints when there is a decoy motif present in the local vicinity of the palmprint.

For example let there be an RdRP containing motifs A, B, and C, with a proximal decoy sequence (E).

EEEEEEEEE-----------------------------AAAAAA------------------------BBBBBBBBBBBB---------CCCC

The ABC are in canonical order and can yield a valid palmprint. If the decoy sequence E is a false-positive match to motif B, palmscan will recognize a longer palmprint with BAC order (EAC). While the per-motif scores of EAC are larger than ABC, the overall palmprint is not considered valid due to out-of-order and longer length. This is a known issue in palmscan.

To overcome this, as an error-fallback for RdRP input sequences, a local DIAMOND search of the input sequence against palmDB can retrieve a potential ABC sub-sequence match which then has a detected palmprint.

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