Amin Allam
Lecturer (Doctor), Computer Science Department, Faculty of Computers and Artificial Intelligence
a.allam@fci-cu.edu.eg (email)
ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings
I implemented the complete efficient system for “ERA”, constructing suffix trees for very long strings. ERA indexes the entire human genome in 19 minutes on an ordinary desktop computer. For comparison, the fastest existing method needs 15 minutes using 1024 CPUs on an IBM BlueGene supercomputer. I implemented these efficient variants of the system: a) Serial: for single-core processor. b) Parallel shared-memory: for multicore processor. c) Parallel shared-nothing: for linux cluster. A research based on this system has been published in the Proceedings of the Very Large Database Endowment, a top-ranked journal in the database area, under the title: E. Mansour, A. Allam, S. Skiadopoulos, and P. Kalnis. "ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings". PVLDB 5(1):49-60, 2011. The system is available here.