miRNA aligment with miRBase parameters

Question

[biofalconch]

Hello all

I have been trying to replicate the alignment made by miRBase under their parameters, only to find that ncbi-blast is unable to do it since it only has a minimum word-size of 7 (and miRBase uses 4). Any thoughts on how I can do it? Also any suggestions when it comes to miRNA datasets alignment to miRBase?

[boczniak767]

At miRBase you could use SSEARCH to align short sequences to miRNAs. So maybe try to find standalone implementation of this.