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miRanda
miRanda is an algorithm which helps to detect potential target sites in the genomic sequences. The piRNAs are supposed to occur in the repetitive sequences of genome. This analysis tool help researchers to find out the complementary sequences of piRNAs in repeat database.

Reference: Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression Nucleic Acids Res. 36,D149-53 (2008)


piRNA Vs Repeat - By Accession number

 By Accession number Help   

Search by entering piRNABank Accession number or NCBI Accession number and the details of repeat sequence.


Example (piRNABank Accession)      Example (NCBI Accession)
            piRNABank or NCBI Accession number
            Repeat sequence details

Default Parameters:

Gap-Opening Penalty = -8.0

Gap-Extend Penalty = -2.0

Score Threshold = 50.0


Energy Threshold = -20.0 kcal/mol



 


piRNA Vs Repeat - By Chromosome number

  By Chromosome: Help   

Please enter the details of piRNA sequence and repeat sequence. piRNA sequence will be aligned against repeat sequence.
(This search may take several minutes. please enter shorter stretch of chromosome.)


piRNA sequence details Repeat sequence details

piRNA Organism     
Chromosome
Position (bp) Example From   To



Repeat Organism
Chromosome
Repeat Class
Position (bp) Example From   To


Default Parameters:

Gap-Opening Penalty = -8.0

Gap-Extend Penalty = -2.0

Score Threshold = 50.0


Energy Threshold = -20.0 kcal/mol