[EMBOSS] dbxfasta and seqret

[Peter Rice]

Weizhong Li wrote:
> Does anybody know how to use seqret to fetch fasta sequences from the 
> index database by dbxfasta?

You need a database definition. Seqret will use this to find the new index files 
and retrieve entries.

Define a database that points to your dbxfasta index and data files (in your 
~/.embossrc file or in the global emboss.defaults.file)

DB mydata [
   type: "N"
   format: "fasta"
   method: "emboss"
   dir: "/data/path/in/full"
   indexdir: "/index/path/in/full"
   comment: "DBXFASTA index of embl"

# if you used a different name when you indexed the database:
   dbalias: embl
]

Then seqret mydata:x12345 will retrieve entry x12345 in FASTA format.

regards,

Peter