generate contigs from forward and reverse reads?

[Avery louie]

Hey all,

I am trying to generate some contiguous sequences from a forward and reverse read of the cloning site in pUC18 with m13 primers.  Is there an easy way to do this?

So far my approach has been to clustalo the the forward and antiparalell of the reverse sequences, but clustalo is not really good at this, as it tries to get the best fit where both sequences overlap the whole length of the sequence, like this:

aaa---t---c---aa

aaagctacccaa

when really I want:

aaatcaa---------------

--------aaagctaccaa

Let me know if you know the way!

A

[Sean Bradley]

Hi Avery. If you include the expected reference sequence in your alignment then clustal should be able to figure things out more. Its still not easy though, and often has to be done by eye and then reassembled. 

align:

>forward Read

>revComp of Reverse Read

>forward Reference sequence

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[Avery louie]

hmm.  fortunately I have a reference sequence.  I will have to try it.

--A