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Generate consensus sequence without considering gaps

Hello.

I have a file with aligned amino acids like below. Each sequence is a fragment of the same protein, therefore, they are identical in some regions.

>seq1
-APQALVARPHVTAPSARRSSRPLLMR---
>seq2
-----LVARPHVTAPSARRSSRPLLMRAAG
>seq3
--PQALVARPHVTAPSARRSSRPLLMRA--
>seq4
SAPQALVARPHVTAPSARRSSRPLL-----

I would like to merge all sequences in one, generating a larger one.

I have tried to use seqinr::consensus in R, but as the gaps ("-") are more frequent than the aminoacids, I don't get the complete protein:

> consensus
--PQALVARPHVTAPSARRSSRPLLMR---

Can anyone help me with this issue, please?

seqinr r consensus fasta
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updated by Mark Mark • written by Nathan • Nathan

1 answer

Use the EMBOSS suite of tools, I think EMBOSS Cons will do this with lots of options. https://www.bioinformatics.nl/cgi-bin/emboss/help/cons

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written by Mark Mark

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