Tools -> Piano
Piano
1. INTRODUCTION
The program Piano is developed for predicting piRNAs. This algorithm uses piRNA-transposon interaction information. Support vector machine (SVM) is applied on these features. Transposon sequences are required. The SVM classifier can be used in a wide range of species including human, mouse, rat, fruit fly and insect pests.
2. INSTALLATION
Download and unpack the Piano folder to a desired location on your computer. We provide Piano as executable (.sh) file that runs on Linux system. Before the prediction please make sure your computer has installed these third-party software, which including Seqmap, RNAplex and LIBSVM (PERL version).
Seqmap (http://www-personal.umich.edu/~jianghui/seqmap/)
RNAplex (http://www.bioinf.uni-leipzig.de/~htafer/RNAplex/RNAplex.html)
LIBSVM (http://www.csie.ntu.edu.tw/~cjlin/libsvm/index.html)
3. INPUT FILES AND OUTPUT FILE
The format of your input sequence should be like this:
>t0000001_435008
TGGAATGTAAAGAAGTATGGAG
>t0000002_262222
TGGAATGTAAAGAAGTATGG
>t0000003_134962
TGGAATGTAAAGAAGTATGGA
>csug10_LTR/Gypsy_+_2381_2433
TATGTATCTATGTATGTGTATGTATATCTATATATATTATAAATATTTATAT
>csug1000_SINE_+_3941_4060
ATCTGTACTAATATTGTAAATTTGTTTGTTGGGAGAAATCTCTGGAACTACTGAACCAATGTTG
>csug100001_DNA/TcMar_C_6517_6596
CTCTAGCTCTATCTGTATGTATATATATTTATATATGTGTTTACAATATATACGTGTATGTAAATATAC