Multiple Sequence Alignment

Question

[Sanju]

How to import clustalw output(.aln file) to R? My sequences are in fasta format.I used the following code

> library(seqinr)
> myseqs <- read.alignment("seqs.fasta", format = "fasta")

I got an error like this

Error in read.alignment("seqs.fasta", format = "fasta") : 


File seqs.fasta is not readable

I am using windows7 operating system. How to save clustalw output in windows and how can I import this aligned file in to R?

[Neilfws]

You need to clarify this question, as pointed out in the answer from pasta. If you want to import .aln, why are you trying to read .fasta?

[Yogesh Pandit]

also are the R script and the input file in the same working directory? else try putting the complete path to the input file

[Sanju]

@neilfws what clarification you need?

Answer 1

[Pasta]

You want to import an *.aln file but you use a Fasta file ?

If you do want to import a *.ALN file then:

MyAln <- read.alignment(file = system.file("Seqs.aln", package = "seqinr"), format= 'clustal')

[Sanju]

@pasta I tried your code. But same error is getting . I run clustalw from embl-ebi . I got the alignment. But I don't know how to save this alignment file in to my system. I clicked on "download alignment file". But file is saving as .clustalw extension.How to change this extension to .aln. I think , then only I can import *.aln file to R.

[Pasta]

ALN and Clustalw formats are the same they just decided to get people confused :) So just rename your file "MySeqs.clustalw" to "MySeqs.aln" and then run the command I posted above

[me.sr1510]

i tried the above command but it is giving the following error

Error in read.alignment(file = system.file("b.aln", package = "seqinr"),  : 
  File  is not readable

i even tried to change the permission n all but nothing is working out

[WouterDeCoster]

Try with the full (absolute) path to the file.

[me.sr1510]

Error in read.alignment(file = system.file("/home/example.aln", : File is not readable even after giving absolute path same error is coming

Answer 2

[Leonor Palmeira]

This is just a formatting problem. Clustalw on EMBL-EBI gives you an output in .clustalw format, but 'seqinr' only reads alignments in .fasta format.

You should convert your .clustalw to a .fasta format, with a conversion tool. There are so many conversion tools available out there, I just randomly googled this one:

http://sequenceconversion.bugaco.com/converter/biology/sequences/clustal_to_fasta.php

Then you should read your .fasta file just fine within 'seqinr'.

Answer 3

[User]

"ALN and Clustalw formats are the same they just decided to get people confused :) So just rename your file "MySeqs.clustalw" to "MySeqs.aln" and then run the command I posted above"

Thanks!!! I had this problem for some time. It works!