Dear Modellers, I am a bit confused about the utility of auto_overhang=true usage in salign_multiple_struc.py for MSA computation. Even if i don't use this line, result comes the same as _fit files are generated. Same is the case when i don't use this line before computing the alignment writing the result. Alignment files generated are also same in both these cases, both including the sub-optimal alignments.
Please explain me this difference. Is it that auto_overhang option is integrated in salign_multiple_struc.py and is employed automatically without being called for it.
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
On 12/14/2011 01:01 AM, Ashish Runthala wrote: > I am a bit confused about the utility of auto_overhang=true usage in > salign_multiple_struc.py for MSA computation. Even if i don't use > this line, result comes the same as _fit files are generated.
auto_overhang is designed to handle the case where the two sequences being aligned are of very different lengths, for example trying to align a single chain with a multi-chain protein. A regular global alignment will try to "stretch" the shorter sequence so that its termini will align with those of the longer sequence; auto_overhang reduces the global alignment penalty so that the termini need not align.
If your sequences are of similar length, auto_overhang will have no effect.
Ben Webb, Modeller Caretaker