Hi @All,
short version: Is it possible to specify more arguments in "Full parameter list"-mode, particularly those that're implicitely described in YASRA-mode (match/mismatch rewards and step-size (Z/step))?
long version: I'm dealing with 454 reads and it's crucial to the scenario to have the 5' ends aligned properly (in terms of sensitivity), so all the YASRA-templates comprising heavy gap penalties perform fairly poor as soon as there's a gap nearby the 5' end. However, heading to "Full parameter list"-mode leads to excessive CPU-use, because (presumably) the step-size (default=1?) is left unset. Also, it'd be great to be able to alter not only gap penalties, but match/mismatch rewards as well. (Obviously a mismatch would cause the same problem).
Examples: AAAAAAAAAA (target) AAAAATAAAA (query)
=> I need the alignment boundary to be found at position 1, rather than behind the mismatched T and this cleary doesn't work as long as the mismatch penalty is too large (same applies for gap-open/extend penalties).
Thanks in advance and Cheers, Uwe