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Is there an option like blastp to set word size for short sequences?

Open ZhangBioLab opened this issue 1 year ago • 1 comments

Hi, I would like to know if the length of the amino acid sequence is only 40 to 50, how to set parameters such as word size like blastp for such a sequence?

ZhangBioLab avatar Apr 16 '24 03:04 ZhangBioLab

No, this corresponds to different sensitivity modes of diamond.

bbuchfink avatar May 27 '24 13:05 bbuchfink

More precisely, you can use the --shape-mask option to set the seed shapes manually, e.g. --shape-mask 111111.

bbuchfink avatar Oct 21 '24 18:10 bbuchfink