Alignment of ABCDEF (model .pdb sequence)
to
ABCDEFWWWDEF (transcript)
can often result in ABC---DEF instead of ABCDEF---
This will be corrected with the following 2 changes to PDBMapAlignment.py:
1) The "penalize_end_gaps=False" parameter will be added to the call of pairwise2.align.globalds()
2) Prior to employing pairwise2 algorithms, a trivial alignment will be attempted. Where models and transcript (sub-)sequences already align 1<->1, we will no longer employ alignment algorithms to re-align.
Alignment of ABCDEF (model .pdb sequence) to ABCDEFWWWDEF (transcript) can often result in ABC---DEF instead of ABCDEF---
This will be corrected with the following 2 changes to PDBMapAlignment.py:
1) The "penalize_end_gaps=False" parameter will be added to the call of pairwise2.align.globalds()
2) Prior to employing pairwise2 algorithms, a trivial alignment will be attempted. Where models and transcript (sub-)sequences already align 1<->1, we will no longer employ alignment algorithms to re-align.