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SBRG / ssbio

A Python framework for structural systems biology
http://ssbio.readthedocs.io/en/latest/
MIT License
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Sequence to structure pairwise alignment parameter tuning #11

Open nmih opened 7 years ago

nmih commented 7 years ago

When running QC/QA, the first thing that is done is a pairwise alignment. The quality of this alignment can have a big impact of the result. The setting of gap score and gap extend penalties should be explored to prevent bad alignments -- example to be added later..

nmih commented 6 years ago

Example of how small quality parameters will impact selection of representative structure. 5AQ6 has 87.5% similarity for protein b1973 chain A but does not pass quality check while 1TXL with 87% SI does, due to small differences in the alignment.

1TXL on the left and 5AQ6 on the right image

erolkavvas commented 6 years ago

wow this is fascinating... so each representative structure (5aq6, 1tx1, ... etc) is a different strain of E. Coli? It looks like 5aq6 is BL21, 5XM5 is K12, and 1tx1 is not specified.

nmih commented 6 years ago

Hah yeah actually I should have looked at that too. Thanks for checking it out Erol. Actually I made a typo, it's 1txl (which is K12) not 1tx1. But the strain check should be implemented as well..