[EMBOSS] dbiflat problem on TRU64

Vito Flavio Licciulli flavio.licciulli at ba.itb.cnr.it
Fri Feb 6 11:15:08 UTC 2004


I have a problem with dat database entries indexing with dbiflat. Sometimes 
the found entries are different from searched entries .

When I run for example:
$>seqret embl:u18650
Reads and writes (returns) sequences
Output sequence [rg9401257.fasta]:
$>more rg9401257.fasta
RG9401257 AJ401257.1 Rotavirus G9 partial VP7 gene for outer capside glycoprote
in, strain G9P[8], isolate 414/98
attatggaattaaatttaccgatcactggctccatggatacagcatatgcaaattcatca....

The search entry (u18650) comes from ROD division while the entry found 
comes from VRL division.
This is the embl definition in emboss.defaults:
DB embl [ type: N method: emblcd
                format: embl dir: $emboss_db_embl indexdir: 
$emboss_db_embl/INDEX
                exclude: *.dat  file: *.dat  comment: "EMBL sequences"]

I found the same problem in SWISSPROT too.

We have a Compaq TRU64Unix 5.1a, is something related to the dbiflat for 
this OS (sort problem,....) ? or what else?

Regards
         Flavio Licciulli

Vito Flavio Licciulli                          e-mail: 
flavio.licciulli at ba.itb.cnr.it
System & Database Administrator
Italian EMBnet Node
C.N.R. - ITB Sez.di BARI                Phone (39) 080-5482100/30
Via Amendola 168/5  BARI ITALY    Fax   (39) 080-5482607
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