Question

How to get sequence homology percent from a multiple sequence alignment in DECIPHER?

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reubenmcgregor88 • 0

@reubenmcgregor88-13722

Last seen 3.8 years ago

I have recently carried out a stipple sequence alignment using DECIPHER package in R. The code was fairly simple as follows:

bod_aa <- readAAStringSet("BOD_aa.fasta")

aligned_aa <- AlignSeqs(bod_aa)

BrowseSeqs(aligned_aa)

This worked nicely but I would like some information on the alignment, specifically the percent homology between the different proteins? If possible percent homology to one of the sequences in particular. I.e. I really want to align all the sequences to one "query sequence" and get a percent homology to that query sequence.

Thanks

decipher r protein alignment • 2.0k views

ADD COMMENT • link 6.5 years ago reubenmcgregor88 • 0

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Just to clarify, do you mean that you would like to get a distance matrix?

d <- DistanceMatrix(bod_aa)

And then look at the distances to a specific sequence (e.g., #1)?

d[1,]

ADD REPLY • link 6.5 years ago Erik Wright ▴ 150

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If the distance Matrix looks like this:

BOD1L2 BOD1L1 BOD1
0.8895349 0.9459459 0.0000000

Does that mean BOD1L1 is 94% homologous to BOD1 and BOD1L2 is 88% homologous to BOD1? Or something similar? Sorry for simplicity of questions

ADD REPLY • link 6.5 years ago reubenmcgregor88 • 0

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The outputs of DistanceMatrix, including examples, are described in:

?DistanceMatrix

Generally, it is a matrix containing the distance between each pair of input sequences. The distance is 1 - the similarity (fraction of sites that are identical).

Homology is not well defined in this context, but I assume you mean similarity.

ADD REPLY • link 6.5 years ago Erik Wright ▴ 150

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Ah ok, I will go back to reference material and try and understand more,

Thanks

ADD REPLY • link 6.5 years ago reubenmcgregor88 • 0