[EMBOSS] problems with indexing RDP SSU_RNA aligned version with dbflat and dbifasta

[Tõnu Margus]

Hi, 

 

I fall in to problems when I tried to index alignes SSU_RRNA sequences from
RDP release 9.26  (both fasta and GB format).

Both files are large than 2 GB (fasta is 5GB and is ca 7GB). 

 

It seems to me that dbflat and dbfasta  (EMBOSS rel 2.9) cannot manage with
wiles what are large than 2 GB in my Mandrake Linux 9.2.

 

If this is correct what could be solution?

 

Is it possible to let them index files form stdin?    Someting like   cat
release_9.26_aligned.fasta    | dbfasta   -bla  -bla -blaa  

  

or  must I split it in to  smaller parts than  2GB?

 

If the spliting is only way is there some tool what can do it correctly for
genbanck format?

 

 

 

Thanks in advance

 

Tõnu Margus

 

 

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