[EMBOSS] Problem with dbifasta

[Jon Ison]

Dear Jean

"ABB51209.1" is the sequence version number.
"ABB51209" is the sequence accession number.

NCBI will retrieve sequences using either.
dbifasta indexes the accession (and also ID) only by default.

To index the sequence version (and also gi number),  specify

-fields "sv"

when you run dbifasta and add the field: "sv" to the database definition.

To index both you might need to use

-fields "sv,acc"


Please check what you did against the notes above and get back
if you still have problems.

Cheers

Jon




> Hi, I have a problem and hopefully someone can help me solve the
> mistery.
>
> I have downloaded emboss 3.0 and create the emboss indexes of several
> FASTA formated databases downloaded from NCBI using 'dbifasta'.
>
> I found some entries can not be retrieved using seqret unless some
> 'trick' is used. For example,
>
> In the month.aa.fas file from NCBI, there is an entry called
> 'ABB51209.1'. After dbifasta, I ran 'seqret' and search for
> monthaa:ABB51209, then I got error. If I search for monthaa:ABB51209.1,
> then I found this entry. If I search 'ABB51209' at ncbi.nih.gov and
> specify protein database, then this entry came out with accession number
> ABB51209, with no '.1' at the tail.
>
> Thank you very much in advance.
>
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