Question: In new genome, how is it decided which strand is forward/reverse?
7
gravatar for michael.nagle
2.2 years ago by
michael.nagle90 wrote:

Is there any particular convention to this or is it just a coin toss?

I'm still pretty new to bioinformatics and I'm assuming the decision of which strand is forward and reverse on each scaffold/chromosome is determined by software in some way. How is this decision made?

genomics assembly • 992 views
ADD COMMENTlink modified 2.2 years ago by John Marshall1.4k • written 2.2 years ago by michael.nagle90
4

You'd be surprised how many things come down to coin tosses :)

ADD REPLYlink written 2.2 years ago by Devon Ryan86k

Which is why science is doomed in some countries:
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ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Jean-Karim Heriche17k
2
gravatar for John Marshall
2.2 years ago by
John Marshall1.4k
Glasgow, Scotland
John Marshall1.4k wrote:

I once heard a rumour that the strand that "most" genes get transcribed from gets designated as the forward strand. However one of the previous answers when this has come up on Biostars before suggests that it's about 50%-50% so that most isn't going to work too well.

See also Forward And Reverse Strand Conventions and Conventions For Designating Forward And Reverse Strands for example.

Googling this question leads to various interesting reading including this short article, which notes:

In all human reference chromosomes, as for other eukaryotes, the plus (+) strand is defined as the strand with its 5' end at the tip of the short arm (Genome Reference Consortium, personal communication, March 27, 2012).

…which seems fairly definitive and supports the centromere location discussion in the latter previous thread. But as noted in that thread, historical accidents occur and this doesn't necessarily hold for various particular species…

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by John Marshall1.4k
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