EMBL and Ensembl

[Jack Leunissen]

This is definitely NOT correct. There can be only 1 (one) SQ line per entry
(see the EMBL user manual
ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt).
So it is Ensembl that is introducing the mistake; the EMBOSS are right
in expecting only one SQ in the entry.

Cheers,
Jack

----- Original Message -----
From: "Stefanie Lager" <stefanielager at fastmail.ca>
To: <emboss at embnet.org>
Sent: Tuesday, March 18, 2003 7:12 AM
Subject: EMBL and Ensembl


> Hi,
>
> I have some problems with the EMBL format output from Ensembl. If I
> retrieve a LARGE piece of DNA from Ensembl in EMBL format, the SQ line
> gets so long so it's divided into two SQ lines, this is NOT handled
> correctly by EMBOSS programs! Some EMBOSS programs gives a warning
> about illegal characters, others just incorporates the second SQ line
> in the sequence. It's easy to fix the problem by manual editing, but
> it would be nice to know it this IS standard EMBL format or if it's
> Ensembl that's made a mistake?
>
> ID   1.77242832-92443803    ENSEMBL; DNA; PLN; 15200972 BP.
> XX
> .....
> .....
> .....
> FT   misc_feature    14757170..15200972
> FT                   /note="contig 1.92000001-93000000 1..443803(1)"
> XX
> SQ   Sequence 15200972 BP; 4106479 A; 3111667 C; 3123445 G; 4136833 T;
> 722548
> SQ   other;
>      TAGAACTTGC AAATGAGAAA ACAGAGTTCT GTCAAGCTGT GTTAGTGTTT GCCCAACACA
>        60
>
>
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