The gridaligner is an open source Java implementation of the Smith-Waterman algorithm for biological local pairwise sequence alignment that runs in a distributed environment using the vgrid framework. For aligning, the code of the open source project jaligner is used. Details about the algorithm and its configuration can be found on the jaligner homepage.
Gridaligner grabs DNA sequences stored in a single file (FASTA format) and pairwise applies the Smith-Waterman algorithm on them. The results are written to a csv file. If multiple computes are connected to the grid, the pairwise alignments are executed simultaneous, what should speed up the total execution time.
The intention of implementing gridaligner was to proof that a third party algorithm can be used in a grid environment without changing that code.
I am not sure if pairwise alignment makes any sense in biology, but gridaligner could be easily extended to iterate over parameter combination or whatever makes sense for biologists.
Go to the vgrid download page to get the latest version of the gridaligner:
| Help | Ask a question if you have problems running gridaligner or if you want extra information not provided on that homepage. |
| Discussion | Post on that forum if you have suggestions how to improve gridalgner. |
Wolfgang Wagner / Vienna / Austria
Mail: wolfgang.wagner@iname.com
ICQ: 171259816
| Sourceforge | This site is hosted on sourceforge. http://www.sourceforge.net |
| vgrid | The Vienna grid project. http://vgrid.sourceforge.net |
| jaligner | JAligner project homepage. http://jaligner.sourceforge.net |