[EMBOSS] water exception

[pmr at ebi.ac.uk]

Hi Graziano,

> I have to align two complete mitochondrial genome
> sequences (about 16500 nt long) using water (emboss
> version 2.7.1). I have tried this alignment on a linux
> server with 2 Gbytes of RAM and water returns this
> error:
>
> "Uncaught exception:  Allocation failed, insufficient
> memory available, raised at water.c:126"

It will be virtual memory rather than RAM. Something in your shell will
limit how much memory you can have for water, and it is not limited to (or
by) the physical RAM in the machine.

But this is a huge alignment problem - just to get a "best local match".

You could get fast results with dottup or (perhaps better) polydot. You
need a large wordsize (the shortest identical sequence you expect in a
real match). Polydot can save the best matches as feature tables.

hope this halps,

Peter