[Seqinr-forum] Need help

[Lionel Guy]

Hi Rinkle,

Your interpretation is partly correct. Leading and lagging strands are  
defined by replication, that starts at the origin of replication, and  
proceeds on both arms of the chromosome to the terminus of  
replication. Because DNA is replicated only 5'->3', the leading strand  
of the replication will be opposite on both arms. Thus, when you take  
one (physical) strand and sequence it, you end up with one segment  
(from the origin to the terminus) being the leading strand of  
replication, and the other one (from terminus to origin) being a  
lagging strand.

So, provided that your sequence starts at the origin of replication  
(which is the case for Vibrio, as far as I remember, the genes that  
are located between that origin and the terminus (i.e. the shift in GC  
skew), _and_ that are located on the "+" strand, as well as the genes  
that are located between the terminus and the origin _and_ that are  
located on the "-" strand, are genes located on the leading strand.

For more info, see for example Lobry and Sueoka 2002 (http://genomebiology.com/content/pdf/gb-2002-3-10-research0058.pdf 
). There is an excellent scheme there.

Best,

Lionel

============================================
Lionel Guy
Molecular Evolution, EBC, Uppsala University
Norbyv. 18C, 752 36  Uppsala, Sweden

phone: +46 (0)18-471 6129
fax : +46 (0)18-471 6404
email: lionel.guy at ebc.uu.se
============================================


On 7 Apr 2009, at 7:22 , Rinkle Mohapatra wrote:

> Dear All
> I am working in a project to compare the genomes of  two Vibrio  
> cholerae pandemic strains ElTor N19661 and  Classical O395. During  
> the course of this project, I am required to identify genes that are  
> present in the leading and lagging strands. I have gone through  
> papers and found that identification of the strands is based on  
> their GC skew. I have interpreted as that when the GC skew is  
> positive, the corresponding base pair positions are genes coding  
> from the leading strand. When the GC skew is negative, it  
> corresponds to the lagging strand. I have considered the graphs that  
> are present in the Oriloc website for this interpretation. I would  
> be glad if you can tell me whether this interpretation is correct. I  
> am also interested to know about the role of the identification of  
> “Origin of Replication” and its role in identifying the leading and  
> lagging strand.
>
> Best wishes
> Rinkle Mohapatra
> Banasthali University
> India
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