Question: Lastz Arguments In "Full Parameter List"-Mode
0
Appelt, Uwe • 70 wrote:
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
ADD COMMENT
• link
•
modified 7.5 years ago
by
Bob Harris • 190
•
written
7.5 years ago by
Appelt, Uwe • 70