The tool “Retropred” develped is an automated methods integrating results from PALS, PILER, MEME and artificial neural network (ANN). The pipeline allows rapid detection of genomic repeats and their further assignment as LINEs and SINEs based on conserve pattern.Pals and Piler are used to identify transposable DNA family.Then MEME is run to discover conserved short patterns (50 bp long) present in the identified repeats. From the discovered patterns, binary pattern files are generated.These patterns files are used as input for a trained Artificial Neural Network for classification into LINEs and SINEs. The results are parsed into graphical representation, indicating the location of LINEs and SINEs in the genome. By clicking the corresponding label it is possible to extract the repeat sequence.
:: MORE INFORMATION
Pradeep K. Naik, Vinay K. Mittal and Sumit Gupta (2008).
RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs and SINEs) from the genome by integrating PALS, PILER, MEME and ANN.
Bioinformation 2(6): 263-270.