[BioPython] codons and complements

Tue, 12 Oct 1999 16:01:02 +0100 (WET DST)

Iddo wrote:
 > Once you have a sequence with a '*' in it, it really stops having any 
 > biological meaning. 

I don't think so - there exists biological meaningful sequences  containing stop
codons. e.g. Peptide Chain Release Factor 2 RF2_ECOLI contains a stop codon
which is part of regulation.

>From the SWISS entry:
CC   -!- FUNCTION: PEPTIDE CHAIN RELEASE FACTOR 2 DIRECTS THE TERMINATION
CC       OF TRANSLATION IN RESPONSE TO THE PEPTIDE CHAIN TERMINATION
CC       CODONS UGA AND UAA.
CC   -!- MISCELLANEOUS: THE GENE FOR THIS PROTEIN CONTAINS A UGA IN-FRAME
CC       TERMINATION CODON AFTER 25-LEU; A NATURALLY OCCURRING FRAMESHIFT
CC       ENABLES COMPLETE TRANSLATION OF RF-2. THIS PROVIDES A MECHANISM
CC       FOR THE PROTEIN TO REGULATE ITS OWN PRODUCTION.

And in the complete genome sequencing progress - you still want to treat
stop codon containing sequences as normal sequences until you know if it is
sequencing error or an ancient gene etc.

In the annotation phase of our complete bacterial genome project "Rickettsia
prowazekii" (typhus) http://evolution.bmc.uu.se/~thomas/Rickettsia/ we had
some problems in the beginning because of software not accepting stop
codons in sequences. So we were forced to reinvent several wheels :-(

I still think there must be space for the user/caller to decide about
biological meanings and how to treat stop codons in the middle of CDS
(Coding sequences).

A lot of sequence analysis mix real CDS and ancient genes (former CDS with frame shifts),
e.g. one gene may be expressed in one organism but seems to be on the way
out of another genome. Still there is significant sequence homology, so you
want to compare them with all available tools (DB search, alignment,
phylogenetic trees, profile searches etc.)  (Jan O. Andersson & Siv
G. E. Andersson. (1999) Genome degradation is an ongoing process in
Rickettsia.  Mol. Biol. Evol. 16:1178-1192.)

If I understood Andrews last post this shouldn't be a problem with the
proposed sequence model. 
.. Or maybe I am completely lost again ... ?

c ya
-thomas

-- 
Sicheritz Ponten Thomas E.  Linnaeus Centre for Bioinformatics
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