miRNA aligment with miRBase parameters
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?
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biofalconch
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At miRBase you could use SSEARCH to align short sequences to miRNAs. So maybe try to find standalone implementation of this.