I looked all over cpan but did not find a module to make Minimizers. Therefore I went ahead and made it in Bio::Minimizer.
Minimizers are l-mers of k-mers, where k is the number of nucleotides in a substring of DNA. A minimizer is a substring of a k-mer with length l. The minimizer is lexicographically the smallest l-mer in the k-mer. They were described in a 2004 paper: https://academic.oup.com/bioinformatics/article/20/18/3363/202143
They seem simple but they have some interesting properties, copied and pasted from the 2004 paper in bold. In the paper, w is equivalent to the notation l. Not all properties are discussed here in this post. My comments are inline.
- If two strings have a significant exact match, then at least one of the minimizers chosen from one will also be chosen from the other. This means that in two strings of DNA, if there is an exact match represented by a k-mer, then there will be an exact match in an l-mer.
- If two strings have a substring of length w+k-1 in common, then they have a (w,k)-minimizer in common. This property basically takes the previous property and applies mathematical variables to it.
- A new minimizer occurs about once every half-window width. If you are thinking about breaking down a genome to a sliding window of k-mers, then consider this. If you use minimizers, that genome is relatively well indexed with minimizers instead.
- A minimizer represents a set of multiple k-mers. Ok, so if you have something in genome A that might have a match in B, one fast thing you can do is find all minimizers in genome A and genome B. Find where exact matches are between the genomes, and even some inexact matches, you could find places that have identical minimizers, and extend the alignment from there.
Anyway, please have fun with the module and if it gets more useful over time, I will develop it more.
https://metacpan.org/pod/Bio::Minimizer
https://github.com/lskatz/bio--minimizer
