Sequences in wrong orientation

Olav Hungnes olav.hungnes at labmed.uio.no
Mon Nov 29 19:36:29 EST 1999


I've seen one such submission - I think it was an arenavirus sequence,
and the reason I found it was because I was searching for matches to a
truly palindromic sequence  - in the original grammatical sense - like
"OTTO". One hit, also annotated as arenavirus, made no sense except
for the searched motif - until I noticed that the entire sequence was
submitted backwards. Can this phenomenon have been caused by
misorientation while reading sequence autoradiographs - like reading
the film from the wrong side?

Olav

On Sun, 28 Nov 1999 17:58:43 +0100, "Dr. A.H.C. van Kampen"
<kwekkwek at xs4all.nl> wrote:

>Hello,
>
>The nucleotide sequences in the EMBL should all be in either the sense
>5'-3'(+) orientation or in the anti-sense orientation 3'-5'(-). Does
>anyone
>has any idea how many sequences are submitted to EMBL in the wrong
>orientation, i.e. either only reverse 3'-'5'(+) or complement 5'-3'(-)?
>
>Regards,
>
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--
________________________________________________________________________
Olav Hungnes                                  olav.hungnes at labmed.uio.no
Natl.Inst.of Public Health, Dept.of Virology  olav.hungnes at embnet.uio.no
P.O.Box 4404 Torshov,                          phone: (+47)22 04 25 20
N-0403 OSLO, NORWAY                            FAX:   (+47)22 04 24 47





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