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About the '--masking 0' option #787

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graa4 opened this issue Feb 8, 2024 · 2 comments
Open

About the '--masking 0' option #787

graa4 opened this issue Feb 8, 2024 · 2 comments

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@graa4
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graa4 commented Feb 8, 2024

Hi, I'm curious about why, despite setting --masking 0, the sseq output still contains many results with 'XXXXXXXX'.
like:
AERLDEVAAQRHCLTDRFHGGGQGGIGTGELLEREPXRLDHHVVQGGFETGRRFPCDVVDDLVEGVTDGQFGGDLGDRKAGRLGRQXXGTRHXRVHLDDDQPTVARVDRELDVAAAGVHTHLAQDRDAQVAHPLVFXVGQRHRXXXXXXXXXXHTHRVDVFDRAHHHHVVVAVAHQLEFEFLPAVNRFLDEHVGAGR-GRQPXXXXXXXXVGGVRYPRTQPAHGEARPXXXXXXXXXDRLTHFGXGETHSAPGGFATGLGXDVLEPLPVLAXLDGVXXXADEFHAVLFQHPALVQRDRGVQRGLPTQGRQQGVDLVAPLGLLGDNPLHERRGDGLYVGVVGELRVGHDGGRIRVHQADLQALGAQHPARLSPXVVELARLADDDRPGXXDQHVVXIGATGH
Thank you!

@bbuchfink
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I could not reproduce the issue when using --masking 0. Please double check that your input sequences don't already contain the X.

@graa4
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graa4 commented Feb 27, 2024

Sorry, I just saw your reply now. The amino acid in the sequence I entered was originally U, but Diamond was automatically replaced with X, it looks like this:
VERFLEGSADGHRLAHGLHRSGKEILRPGKLFKREPGHFHHAVIDGGLERSPGLPGDVVGDLVQGIPHGQLGGDLGNGKPRRLGCEGRXPGDPGVHLYDDHLPVGGVDGELDVGPPRLHADFPQNRNRGVPQQLIFPVGQGLGRSHRDRIPRMDAHGVHVLDGADDDHIVHAVAHDLELEFLPAEHRLL-EHDGVNETGIQPALGQFLQFFPVVGHAAPRAAQRERRPHDDRETDLPGNGFHFRHGTRNAAGRNAQPDPLHGIAEQFPVFGFLDDFNTRSDESHAETFEHTRFGHAHRHVQGRLPAQGGQQRVGTL-PL----DHLRHRFGRDRLDIGAVGRFRIGHYCCGVAVDQDNLVPFLAQCLAGLGPGVVELARLADDDGAGSDDQYLSYVGSLGH

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