> ... and also for the record on our RedHat 7.2 based system (kernel > 2.4.2-2smp?), files greater than 2GB have to be piped into formatdb, rather > than supplied as an argument I wrote and send to this list a Perl script for cutting a large size database into pieces .. I test with a "nt" (~ 6GB) and I can supplied it as an argument. It's not a great code, but it's works :) Furthermore, Tim Harsch says that splitting a database reduce the costs of phisical memory ... I think it is not good at all .. because the results are not right ... we are test a local blast cluster (9 DELL Power Edge) and the best performance (reducing costs of time and disk usage) is obtined when split the input files (fasta format obtained via phredPhrap) in equal size of the physical memory available and send separate jobs to each node in the cluster ... I hope you find this useful (for beginners i guess) Greetings > Andy ps: I am so sorry for my bad english :/ -- Sergio Antonio Ahumada Navea mailto:san@inf.utfsm.cl Centro de Bioinformatica - UTFSM http://www.biotec.utfsm.cl/