bbuchfink
About the '--masking 0' option
Hi, I'm curious about why, despite setting --masking 0, the sseq output still contains many results with 'XXXXXXXX'.
like:
AERLDEVAAQRHCLTDRFHGGGQGGIGTGELLEREPXRLDHHVVQGGFETGRRFPCDVVDDLVEGVTDGQFGGDLGDRKAGRLGRQXXGTRHXRVHLDDDQPTVARVDRELDVAAAGVHTHLAQDRDAQVAHPLVFXVGQRHRXXXXXXXXXXHTHRVDVFDRAHHHHVVVAVAHQLEFEFLPAVNRFLDEHVGAGR-GRQPXXXXXXXXVGGVRYPRTQPAHGEARPXXXXXXXXXDRLTHFGXGETHSAPGGFATGLGXDVLEPLPVLAXLDGVXXXADEFHAVLFQHPALVQRDRGVQRGLPTQGRQQGVDLVAPLGLLGDNPLHERRGDGLYVGVVGELRVGHDGGRIRVHQADLQALGAQHPARLSPXVVELARLADDDRPGXXDQHVVXIGATGH
Thank you!
I could not reproduce the issue when using --masking 0. Please double check that your input sequences don't already contain the X.
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