Question: How To Merge Overlapping Two Or More Dna Sequence?
3
gravatar for Geparada
8.8 years ago by
Geparada1.4k
Cambridge
Geparada1.4k wrote:

Hi! I'm analyzing the results of few PCR product sequenced by Sanger method. I have the result using forward and reverse primer. Because the PCR products aren't too long, there are regions that overlaps, so I want to merge this to overlapping sequences to get only one big sequence.

Are there any online tool to do this?

Thanks!

pairwise sanger sequencing • 17k views
ADD COMMENTlink modified 5.6 years ago by ragichedupraveen0 • written 8.8 years ago by Geparada1.4k

Hi! I'm analyzing the results of around 400 PCR products sequenced by Sanger method. I have the result using forward and reverse primer. Because the PCR products aren't too long, there are regions that overlaps, so I want to merge this to overlapping sequences to get only one big sequence. I used  primarily cap 3 but it not good, by DnaBaser i got some contig results but how can i join those sequences,,,,,

Are there any online tool to do this? 

Thanks

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by ragichedupraveen0

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ADD REPLYlink written 5.6 years ago by Pierre Lindenbaum128k
6
gravatar for Pierre Lindenbaum
8.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

The emboss package contains a tool named merger:

This joins two overlapping nucleic acid sequences into one merged sequence.

It uses a global alignment algorithm (Needleman & Wunsch) to optimally align the sequences and then it creates the merged sequence from the alignment. When there is a mismatch in the alignment between the two sequences, the correct base to include in the resulting sequence is chosen by using the base from the sequence which has the best local sequence quality score.

see also the related programs at the bottom of the page (cons and megamerger).

ADD COMMENTlink modified 6 months ago by RamRS27k • written 8.8 years ago by Pierre Lindenbaum128k

Fantastic!

solved my problems.

Thanks

ADD REPLYlink written 5.1 years ago by razip.samian0
2
gravatar for Darked89
8.8 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

This is a small scale DNA assembly. You may try CAP3

This should work if sequences are of good quality. If you got some nasty sequence ends or lots of Ns you will have to use the sequence quality values / Sanger trace files feed to standalone tools, such as gap4 from Staden

ADD COMMENTlink modified 6 months ago by RamRS27k • written 8.8 years ago by Darked894.2k

I really like it because I can overlap more than 2 sequences. Thanks!

ADD REPLYlink written 8.8 years ago by Geparada1.4k
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