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How To Merge Overlapping Two Or More Dna Sequence?

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
• 23,249 views • link
updated by Ram Ram • written by Geparada Geparada

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

• 0 views • link
updated by Ram Ram • written by ragichedupraveen • ragichedupraveen

2 answers

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).

• 154 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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

• 3 views • link
updated by Ram Ram • written by Darked89 Darked89

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

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written by Geparada Geparada

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