I'm having trouble with loading MSP files into ACT. Basically, no matter how I slice it, ACT takes the sequence positions for hits in the sequence loaded at the top of the screen and highlights them in positive frame, even if the blast (tblastx) report had them in a minus frame.
For example, I have a hit in the blast report of "Rcaps_GTA" vs "phi_c31" that puts Rcaps_GTA in a negative frame and phi_c31 in a positive frame. Here's the MSPcruch output line for this hit: 0 32.05 12756 12523 Rcaps_GTA 3576 3809 phi_c31 For the minus-frame hit, the greater sequence position is listed first, then the lesser, and this is how all the minus-frame hits look in the file. But when I load these into ACT with Rcaps_GTA at the top of the window, the hit is highlighted in a positive frame for Rcaps_GTA and in a negative frame for phi_c31 (which ought to be in a positive frame!). I've tried loading phi_c31 at the top of the window, but a similar problem occurs where all the phi_c31 hits are converted into positive frame. Any thoughts on what might be going on? I may be missing something very obvious here as I'm not very familiar with this sort of comparison file, but I can't seem to get these hits in frame. Thanks much. Best, Dave Kysela
