Registered 2009-06-25 by Felipe Scarel

zAlign is a local sequence aligner, especially intended for use with large biological DNA sequences, with more than 1Mbp (Millions of base pairs). It uses the Smith-Waterman exact algorithm with affine gap cost function to perform this task.

zAlign can be used both in distributed (clusters, for example) or standalone environments. Currently it has been tested on Linux and Sun Solaris, using both the MPICH (http://www.mcs.anl.gov/research/projects/mpi/mpich1/) and OpenMPI (http://www.open-mpi.org/) implementations. Ports for other Unix-like environments are highly considered.

The program was originally developed by Rodolfo Bezerra Batista in his MsC thesis, under the supervision of Prof. Alba Cristina Magalhães Alves de Melo, as a student of the Department of Computer Science (CIC), University of Brasília (UnB), Brazil. Later improvements were made by Paulo Renato Castro, Paula Oliveira, Felipe Scarel and Lavir Souza, all undergraduate students from the same university. The project is currently maintained by three developers: Rodolfo Batista, Felipe Scarel and Lavir Souza. External submissions and ideas are always welcome, of course -- why don't you become the next one to contribute and join our team?

Code for the zAlign project is GPL v3 licensed and can be downloaded through the 'trunk' branch (check our 'Code' page). Bug reports and suggestions can be made through the "Bugs" tab above, and any questions you might have can be asked by accessing the "Answers" tab.

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zAlign-related publications:

1) BATISTA, Rodolfo B ; MELO, A. C. M. A. Z-align:An Exact Parallel Strategy for Biological Sequence Alignment in User-Restricted Memory Space. In: IEEE International Conference on Cluster Computing, 2006, Barcelona, Spain.
2) BATISTA, Rodolfo B. ; BOUKERCHE, A. ; MELO, A. C. M. A. A parallel strategy for biological sequence alignment in restricted memory space. Journal of Parallel and Distributed Computing, v. 68, p. 548-561, 2008.
3) BOUKERCHE, A. ; BATISTA, Rodolfo B ; MELO, A. C. M. A. Exact Pairwise Alignment of Megabase Genome Sequences with the Z-align Parallel Strategy. In: 12th International Workshop on Nature Inspired Distributed Computing (NIDISC), Rome, Italy, IEEE Computer Society, 2009.

Project information

Maintainer:
zAlign Development
Driver:
Not yet selected
Licence:
GNU GPL v3

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Programming languages:
C, C++

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Latest version is 0.9.1
released on 2009-08-16

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