# Reverse complement of reconstruction model for assembling reads

One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this problem is the reconstruction model, which calculates the minimal edit distance between a possible superstring (that contains all fragments) and each one of the fragments. What I don't understand yet is the fact that when calculating the edit distance for a given fragment, it's necessary to calculate the edit distance for the reverse complement of that fragment.
An example of a fragment and its reverse complement could be:

ACTGTCC fragment
TGACAGG complement (the complementary strand as we know)
GGACAGT reverse complement

According to the book I'm reading the ideia behind it is to find a superstring as short as possible that either the given fragment or its reverse complement must be an approximate substring of the superstring. I know that many mathematical/computational models don't have a biological sense for their way of soluting a biological problem, but this recontruction model I could think it's biologically reasonable to find a string that contains all the fragments of a certain region of a DNA sequence, and all the complement fragments, after all when assembling we can find both strand sequence. But a reverse complement is not something that exist for a given sequence, unless it has suffered some kind of break-recombination event, which is something not expected, mainly when talking about conserved regions. Do you any idea why this model takes into account the reverse complements ? Thanks in advance.

• Isn't this just a case of keeping everything straight with respect to 5'>3' direction? If a read matched "TGACAGG" this would not correspond to either strand of your example, because writing it like that implies that it is 5'-TGACAGG-3' unless it is made explicitly clear that it is the bottom strand of a duplex. – Alan Boyd May 21 '13 at 5:24
• So you're saying that in fact the model see every fragment in 5'->3' direction? It doesn't consider the real existence of a reverse complement, but simply uses it because the reverse complement is a way of seeing the complementary strand of a given fragment with 5'3'direction? I'm sorry about the slow reasoning. – Heidi Garcia May 21 '13 at 14:36
• Yes, if you have a read (which will be by convention 5'>3') then you can search for it directly on the top strand of the target (also 5'>3'). If you need to look for it on the other strand of the target you can't simply search on the complementary because this is 3'>5', so you derive the reverse complement. It's just the equivalent of turning the dsDNA sequence (on the page) through 180 degrees. – Alan Boyd May 21 '13 at 15:52
• Nice! Thank you very much, Alan. You helped me a lot. – Heidi Garcia May 21 '13 at 18:55