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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
