[EMBOSS] Emboss package - file size limitations

[Peter Rice]

Hi Sumit,

> Is there a limit to the size of files that I can use, and is there a different
> limit on the web and command line usage.

EMBOSS has no hard coded limit on sequence or file size. The operating system 
may have problems with 2Gb file size, and the EMBLCD indexing system we use 
for database indexing in EMBOSS 2 has a 2Gb file size limit (4 byte file 
pointers are part of the index format) - there will be a new indexing system 
in beta release with EMBOSS 3 that will have enough space for large file offsets.

Some algorithms will have limits, depending on the memory (real and virtual) 
on your machine.

> Actually I had the same question for GCG tools.

I believe sequence length is still up to 350kb unless you have the source code 
(when I was at Sanger I routinely rebuilt GCG with 750kb as the maximum 
sequence length so the genome sequencers could still use it on their own 
sequences!) A future release of GCG is supposed to increase this.

Hope that helps,

Peter Rice