[EMBOSS] problems with indexing RDP SSU_RNA aligned version with dbflat and dbifasta
Tõnu Margus
tmargus at ebc.ee
Sun Mar 13 16:34:12 UTC 2005
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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