Isolate a stretch of residues in one or more sequences in an existing alignment.   (New Discovery Script)

Created for use with Build Homology (Modeler)

This Discovery Script (compatible with DS 3.5) is designed to segregate the selected residues in an alignment from the other sequences in the alignment.

This is helpful because Modeler (Build Homology) will create restraints to all residues that are aligned to residues in the target sequence.  To exclude any template residue  from this the alignment must be adjusted so as to disrupt the alignment locally, while maintaining the alignment on both sides outside of this region.  Manually this can be done by adding n gaps prior to the residues to be isolated, and for the other sequences in the alignment and n gaps after the stretch of sequences to be isolated (for each sequence).

This script accomplishes this automatically.

For example:

1) Have a sequence alignment open in Discovery Studio.

2) Select residues (red) to segregate these from the rest  (lower case letters  indicates the target sequence)

frketiyflfnd

FRKA.GYFLFSD

FAKESVYFLFND

FVPADVYTLFSD

3) After running the script the alignment will be

frketiyfl.......fnd

FR.......KA.GYFLFSD

FAKESVYFL.......FND

FV.......PADVYTLFSD

With this alignment Modeler will rely on the structure of the loop in sequence 3 to construct the conformation of ketiyfl.

The zip files includes:

• ModelerAlignmentIsolation_v1r4.pl
• icon_ModlerSegregate.png
• this document (ModelerAlignmentIsolation.rtf)

Note, the script can be installed into DS using the Scripts pulldown using Edit/Preferences/General/Script Commands, and after that is done the new function can be added to any toolbar using

Edit/Preferences/General/Toolbar.  Or, more simply just drag the .pl file into DS script window.