[EMBOSS] dbifasta and ncbi formats

[Tõnu Margus]

Hi,

 

Sorry for trivial question. What are available „formats” for ncbi fastA
format ?


ncbi

(| formats)

 

I don’t figure out, how to specify these (| formats)

 

If I run dbifasta and choose –idformat ncbi  then after creating database
index seqret returns sequences only when I specify NP_414542.1 and not by gi
number.  How can I use the gi number for retrival as well?

 

Example header of FastA flatfile

 

>gi|16127995|ref|NP_414542.1|     thr operon leader peptide [Escherichia
coli K12]

 

AND 

 

Database definition is here

 

DB ec [

   type: P

   dir: /home/db/coli

   method: emblcd

   format: fasta

   file:ecoli_p.faa

   comment: "E.coli proteom from NCBI"

] 

 

 

Thanks 

Tonu