"RNA-RNA interaction (RRI) is ubiquitous and has complex roles in the cellular functions. In human health studies, miRNA-target and lncRNAs are among an elite class of RRIs that have been extensively studied and shown to play significant roles in various diseases including cancer. Bacterial ncRNA-target and RNA interference are other classes of RRIs that have received significant attention. Accordingly, RRI bioinformatics tools tailored for those elite classes have been proposed in the last decade." [1]
Computational models of RRI ( piRNA, BPMax, BPMaxW) are important but very expensive in time and memory space.
• Time Complexity: O(𝑁^3𝑀^3)
• Space Complexity: O(𝑁^3𝑀^3)
For further information refer to Ebrahimpour et al.
AlphaZ is an open source tool-set for program analysis, transformation and parallelization in the Polyhedral Equational Model. It is being developed by the Mélange group at CSU, and uses an equational language called Alpha/Alphabets.
Setup eclipse plugin using this link
This repository includes:
- script.sh
- This is the script for running eclipse via terminal
- BPMaxW.ab
- Alphabet code for BPMax equation
- BPMaxW.cs
- script for compiling the .ab file
[1] Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model
Feel free to contact me: Email: pooria[at]colosate[dot]edu