[EMBOSS] dbiflat and entret...

[Jérôme Laroche]

Hi Ted,

Try this:

1. dbiflat -fields taxon
choose the right format of your flatfile: entry format

2. Add the following lines in your .embossrc file:

DB swtest [
    type: N
    method: emblcd
    format: genbank <-specify the format
    dir: path    <- the path of your database
    indexdir: path   <-the path of your index files
    fields: org		<-the field you have indexed
]
3. seqret swtest-org:homo

I run a couple of test and it works. But you should knwo that not all 
words in the field  ORGANISM are indexed. Just those of taxonomic 
significance.

So in a genbank flatfile containing the following organism field for 
two entries, the keywords 'Rhizobium/Agrobacterium group'  and 'dsDNA 
viruses, no RNA stage' use together or alone were not recognized even 
if they are in the organism field.

   ORGANISM  Agrobacterium sp.
             Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
             Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
  or

   ORGANISM  Chlorella virus
             Viruses; dsDNA viruses, no RNA stage; Phycodnaviridae; 
Chlorovirus.



Good luck!


Jérôme
Centre de bioinformatique
Pavillon Charles-Eugène-Marchand
Bureau 4233d
tél: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca