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I have Ensembl compara gene tree alignments (Compara.gene_trees.57.fasta.gz downloaded from ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/) in nucleotide format. According to documentation, it says that the file "contains the peptide alignment for every genetree in fasta format".

I was wondering what might be a handy tool to obtain the corresponding amino acid alignments from the file.

Thanks,

Ikram

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  • $\begingroup$ The file is gzipped, so use a tool like 7zip or WinRAR to unzip it. After that, just open the fasta file in any text reader..? $\endgroup$
    – Armatus
    Commented May 15, 2014 at 21:11
  • $\begingroup$ Thanks Armatus for the comment. In fact I can view the file using zless in ubuntu. The problem is that the data is in nucleotide format (AGTC...) and I want it in amino-acid format (NGHIK... etc). I guess that, since the data is coding sequence, no frame shifts are needed and just a mapping from DNA-to-Protein might work (But I am not sure, and just want to confirm it before writing some code for it) $\endgroup$ Commented May 15, 2014 at 23:38

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As a general rule, both within and without the world of bioinformatics, public FTP sites contain README files tat explain what each file offered by the FTP server contains. The file README.protein_trees states:

Compara.gene_trees.{release}.emf.gz

                       contains the peptide alignment for every genetree in emf alignment format

Compara.gene_trees.{release}.fasta.gz

                      contains the peptide alignment for every genetree in fasta format

This means that both Compara.gene_trees.57.emf.gz and Compara.gene_trees.57.fasta.gz contain the protein alignments. I had a quick look at the files and it looks like Compara.gene_trees.57.fasta.gz actually contains nucleototide sequences but Compara.gene_trees.57.emf.gz does indeed contain a protein alignment:

$ zgrep -m 1 AAAAASAAAT Compara.gene_trees.57.emf.gz.crdownload 
SAAA-AHS-AGTAAAAA--AA--AAAAASAAAT-ASAATAI-SASSA-ASAAT-V----AAASVAA-HAFAS---ASAAASAAAAA-TIVAAAAX-SAASIYSAAAA-YAA--AASAS-ASAASAS-ASAASSSSSARS-AAS

So, to answer your question, the file you want is the .emf.gz one.

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