How find tool algorithm works in OVE

[tnrich]

Copied from an email with @pmaen:

I am currently working on an open source bioinformatics tool and need to be able to search for sequences in circular plasmids. I have seen that your tool Open Vector Editor is capable of doing this, but I am not familiar with JavaScript. Could you perhaps explain to me what approach you used to implement this function?

Example of what I mean

Basically, my problem is that when searching for a string in the plasmid, the string I am looking for could be, for example, the last 30 bases of the plasmid and the first 20 bases of the plasmid, which would be a 50 nt sequence on a circular plasmid, but I couldn't find a way to implement this in my tool.

Thank you in advance.

Kind regards
@pmaen

[tnrich]

Hi @pmaen, Here's where that code lives:

The findSequenceMatches function:
https://github.com/TeselaGen/ve-sequence-utils/blob/master/src/findSequenceMatches.js

Test code showing how the function is called:
https://github.com/TeselaGen/ve-sequence-utils/blob/master/src/findSequenceMatches.test.js#L110

If you look in the code, you'll see the "trick" for finding matches that cross the "origin" of the sequence:

Basically if the seq is circular, we duplicate the seq so we can find matches that span the origin. At the end of the function we then modulate any ranges that have ends that are "too long"

as well as remove any duplicates caused by the doubling of the sequence:

Hope that all makes sense for you!
-Thomas

[pmaen]

Thank you very much for the thorough explanation. That helps a lot.

Kind regards
Paul