BPLA kernel 1.1
BPLA kernel (Base-pairing profile local alignment) is a powerful method that evaluates the similarity between a pair of RNAs taking into account secondary structure information. Based on the accurate similarity calculated by BPLA kernel, you can perform a broad range of structural RNA analysis, including family prediction, hierarchical clustering, and remote homology search. The method is applicable not only to classical genomic screens, but also to unannotated noncoding transcripts produced by next-generation sequencing technologies (RNA-seq).
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BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S3. doi: 10.1186/1471-2105-11-S7-S3.
Robust and accurate prediction of noncoding RNAs from aligned sequences.
Saito Y1, Sato K, Sakakibara Y.