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Merge multiple overlapping consensus sequences

Hi All,

I have 10 consensus sequence files which have some overlapping regions between them. I would like to merge all of them to generate single consensus fasta file. I have looked into emboss merger but it takes only two input files. How can I achieve this? Which software should I use?

Thanks in advance!!!

assembly consensus
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updated by Ram Ram • written by kspata kspata

2 answers

Do a multiple sequence alignment (MSA) with all 10 and then export a consensus. Most MSA programs can be used for this.

• 1 views • link
written by GenoMax GenoMax

Thanks @genomax!!! I used Clustal Omega to align the consensus sequences with each other. Downloaded the JalView results and obtained a consensus sequence.

• 2 views • link
written by kspata kspata

Perfect. So all done then. I will move my comment to an answer that you can accept to provide closure to the thread.

• 1 views • link
written by GenoMax GenoMax

For fasta files, add all to one file, 

cat *.fas > conca.fas

Then in with python:

python3.4 combineSequences.py -f conca.fas -r myout.txt

The script is in: https://gitlab.com/ferroao/msa

• 0 views • link
written by ferroao • ferroao

How is this python script better compared to established well tested MSA tools?

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written by Ram Ram

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