[Biojava-dev] [BioJava - Bug #3352] (New) SEQRES alignment wrong when disordered region begins and ends with same amino acid

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Issue #3352 has been reported by Steven Darnell.

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Bug #3352: SEQRES alignment wrong when disordered region begins and ends with same amino acid
https://redmine.open-bio.org/issues/3352

Author: Steven Darnell
Status: New
Priority: Normal
Assignee: biojava-dev list
Category: structure
Target version: 
URL: 


A misalignment occurs when SeqRes2AtomAligner aligns the SEQRES and ATOM sequences in 3T5N, chain A at 112..163. After LYS 112, the disordered region begins with VAL then the next ordered region begins with VAL 163.

The order should be (ATOM UPPER, seqres lower):

KLKSK(112)[v]irte...dgvvrV(163)WDVK

but the alignment is:

KLKSK(112)V(163)irte...dgvvr[v]WDVK

[v] and V(163) have swapped positions in the group list, which breaks the logical assumption that the group order will not change. The problem arises from using sequence representations of SEQRES and ATOM lists for the alignment. Can this problem be resolved without significant architectural changes to SeqRes2AtomAligner?


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