[chimerax-users] align peptide to model sequence

[Eric Pettersen]

Hi Ilse,
	Well, you could use search() I suppose.  You could also use the SmithWaterman or NeedlemanWunsch modules to perform local or global alignments (respectively) of your peptide sequence to your model sequence (example usage of both in match.py in the match_maker module).  All these sound like they may be overkill.  You could simply place the peptide sequence at the left end of the model sequence and count how many matches there are, move it one to the right and count the matches, etc. to determine the best placement and maximum number of matches.  That way you don't have to deal with constructing a grep pattern and parsing the result from search, or the gapping of the sequences from the alignment algorithms.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 15, 2021, at 8:17 AM, Lagerwaard, I.M. (Ilse) via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi everyone,
>  
>  
> I want to write a script that can align the sequences of peptides to a model sequence and return the identical residues. Because I am new to programming, I could really use some help to get started. Could I use the search() method of the Sequence class for this? And if so, how could I go about this? 
>  
>  
> Kind regards
>  
> Ilse Lagerwaard
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