Generate Consensus Sequence from Pairwise Alignment

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5.8 years ago

kspata ▴ 80

Hi All,

I am aligning a consensus sequence with a reference genome by pairwise alignment. Is there a tool which can generate a consensus sequence from pairwise alignment?

Is there any way to generate a consensus sequence from a blast alignment result?

Any help will be appreciated.

Thanks in advance!!!

alignment Consensus Blast • 2.7k views

ADD COMMENT • link 5.8 years ago by kspata ▴ 80

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Most multiple sequence alignment tools should be able to align 2 sequences and generate consensus. Are there gaps and such in your sequences?

As for generating alignments from blast results look here for options.

ADD REPLY • link 5.8 years ago by GenoMax 141k

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Hi genomax,

I performed nucleotide BLAST alignment on the consensus sequence (single fasta file) and the reference sequence. I found gaps and mismatches in the alignment. My aim was to generate a consensus sequence from this alignment result.

On Clustal Omega I saw their suggestion to use pairwise alignment for alignment of 2 sequences. Is it still okay to use a MSA for this?

ADD REPLY • link 5.8 years ago by kspata ▴ 80

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