pirnaPre

Input file for generating the mode: example



Input file for prediction: example



   


Input Files Format Description:
Each line represents an instance, with a label of -1 / +1 indicating a pre-defined false / true piRNA-mediated cleavage sites on mRNAs. The pair : gives a feature value: is an integer starting from 1 and is a real number.
The feature values for 86-dimensional features are required:
   1 - quantitative values: the number of target fragments detected in the Miwi complex mapping to a region ranging from 150 nt upstream to 150nt downstream of the given site (see Figure 1 for details);
   2 - quantitative values: the number of distinct piRNAs with 5' ends located exactly 10 nt downstream of the given target site basee d on base-pairing complementarity to the flanking sequence (see Figure 1 for details);
   3 - {0,1}, about conservation: 1 means that the given target is located in 3'UTR of the host mRNA
   4 - {0,1}, about conservation: 1 means that the given target is located in 5'UTR of the host mRNA
   5 - {0,1}, about conservation: 1 means that the given target is located in coding region of the host mRNA;
   6 - {0,1}, about repeat: 1 means that the given target is located in simple repeat;
   7 - {0,1}, about nucleotide usage: 1 means that the nucleotide on 10th position upstream of the given cleavage target is A;
   8 - {0,1}, about nucleotide usage: 1 means that the nucleotide on 10th position upstream of the given cleavage target is T;
   9 - {0,1}, about nucleotide usage: 1 means that the nucleotide on 10th position upstream of the given cleavage target is C;
   10 - {0,1}, about nucleotide usage: 1 means that the nucleotide on 10th position upstream of the given cleavage target is G;
   11~86 - {0,1}, about nucleotide usage: similar with 7~10th features, but on the following 19 downstream positions. As a whole, the 7~86th features correspond to the nucleotide usage of the 20nt sequence with the target site exactly in the middle.

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