cudalign

We have hosted the application cudalign in order to run this application in our online workstations with Wine or directly.

Quick description about cudalign:

CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information:
[1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. IEEE Transactions on Parallel and Distributed Systems, vol. 99, PrePrints, 2012
[2] Edans Sandes, Alba Melo. Smith-Waterman Alignment of Huge Sequences with GPU in Linear Space. IPDPS 2011: 1199-1211
[3] Edans Sandes, Alba Melo. CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences. PPOPP 2010: 137-146

The latest source code can be found in Github. See the MASA project at https: //github.com/edanssandes/MASA-CUDAlign.

Audience: Science/Research.
User interface: Java Swing, Command-line.
Programming Language: C++.
Categories: