I want to create fragments given a query sequence of any length and the fragment extracted should be of same sequence. So just picking fragment without applying scoring scheme.
How can I do this?
(My reply seems not to have been posted, so here it is again.)
With the caveat that I’m not that experienced with the fragment picker, I’m not aware of any flag or option which will enforce 100% sequence identity.
What you can do instead is use the SequenceIdentity scorer to score fragments based on how many amino acids they have in common. Using just this scorer, all of your top fragments will have identical or near identical sequences. To handle cases where there may be more than 200 likely fragments with the same sequence, you can use other scorers along with it, but with a really high weight on the SequenceIdentity scorer, so fragments will be sorted primarily by sequence identity, but then secondarily by other factors.