I have a string of DNA bases and I need to count the number of times I have two identical bases at a certain distance from each other.

1 view (last 30 days)
Nitzan Kahn
Nitzan Kahn on 18 Jun 2018
Commented: Nitzan Kahn on 18 Jun 2018
I have a string of DNA bases and I need to count the number of times I have two identical bases at a certain distance from each other. For example- number of times for 'AA', 'AXA', 'AXXA' and so on.. Would love some help with finding the right function.

Sign in to answer this question.

Accepted Answer

Guillaume
Guillaume on 18 Jun 2018
sum(regexp(yourchararray, 'A[^A]{0,2}A'))
2 being the maximum distance between two A (and 0 the minimum). The regexp says match A followed by 0 to 2 not A, followed by a A.

More Answers (0)

Categories

Find more on Genomics and Next Generation Sequencing in Help Center and File Exchange

Tags

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!