[EMBOSS] question about index refseq database

Henrikki Almusa henrikki.almusa at helsinki.fi
Fri Oct 24 06:38:48 UTC 2003

On Thursday 23 October 2003 23:44, Jean Mao wrote:
> I have the following 2 files for refseq nucleotide and protein databases
> from NCBI:
> ----------------------------------------------
> rscu.gbff.Z	GenBank flatfile view (nucleotide sequence with annotations)
> 	rscu.gnp.Z	GenPept flatfile view (protein sequence with annotations)
> -----------------------------------------
> When I run dbiflat, should I enter GB or REFSEQ when prompt 'Entry format'?

I haven't used refseq files but. i'd suggest you use refseq (remember to unzip 
files first). 

> Also, in the .embossrc file, is the following entry correct (method=emblcd
> and format=genbank)?
> ----------------------------------------
> DB refseqnt [ type: N method: emblcd format: genbank dir:
> $emboss_db_dir/refseqnt indexdir: $emboss_db_dir/refseqnt file: "*.gbff"
> release: "1.0" comment: "update 23/Oct/03" ]

Method might be refseq as well. Unfortunately this isn't covered by admin 
manual in emboss web site. I assume that you have two directories so that 
there is another entry in .embossrc for protein file.

Hoope this helps,
Henrikki Almusa

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