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

[SC]

Hi Avery,

try this online assembly program:

http://egassembler.hgc.jp/cgi-bin/eassembler4.cgi

 

Good luck,

Stacy

[Nathan McCorkle]

you could probably spin your own checkermerger with bioPython

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[Mac Cowell]

Have you asked at http://www.biostars.org/ or seqanswers.com?  I bet someone over there knows.

Mac

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