How to translate CDS to an amino acid sequence

Question

[Max]

How to translate CDS to amino acid sequence? This site shows CDS and translations but no explanation on how to get there.

[cmdcolin]

the link you are posting provides the translated amino acid sequence for the CDS. If you had just the DNA letters, and wanted to translate, you can paste into something like https://web.expasy.org/translate/

[vvasta]

I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number with DNA /prot aligned line by line

Thanks

Valeria

Answer 1

[brian.fristensky]

Each CDS has a link with the tag "/protein_id", which leads to the corresponding GenBank protein entry.

If what you want is to get all of the proteins into a single FASTA file, go to the Related Information box at right and click on Protein. This will bring up a list of all proteins in the viral genome. Select all proteins, and then open "Send to" at upper right. Choose File, Format FASTA, and Create File. This will save your file to disk.

Note that some of these CDS features include gaps (multiple N's) representing regions of this strain for which sequence is not available. These are represented as X's in the proteins.

This entire process can be automated with a few clicks using the BIRCH system. The Sequence Dataset tutorial includes automated extraction of CDS features, followed by translation of DNA to protein.

Answer 2

[Jeremy]

Click on FASTA in your link to get the FASTA nucleotide sequence. You can then copy and paste that sequence into SnapGene Viewer, then click on the "Show translations" button on the left. You can choose which reading frames to view, but SnapGene will color the predicted reading frame in orange.

Alternatively, you can use translate() in the Bioconductor Biostrings package in R. You can trim 1 or 2 nt to change the reading frame. You'll first need to convert your nt sequence to a DNAStringSet. You can use something like the following:

seq = DNAStringSet('[your sequence]')
aa = translate(seq, if.fuzzy.codon = 'solve')
aa

SnapGene Viewer (free)

Biostrings

[Max]

But what if I wanna translate them by myself? Is there a universal translation table or something similar?

[cmdcolin]

there are multiple translation tables or "genetic codes". here is a good link showing many of them. almost all life uses the "standard code" but there are interesting exceptions https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

[Max]

I guess the standard table should work for all cases really well?

[Jeremy]

Here is a Wikipedia article with codon tables. Any biochemistry textbook will also include a codon table. Remember that the CDS starts with methionine (M) and ends with a stop codon.

DNA and RNA Codon Tables

[Max]

The link which you send is invalid but I think you wanted point to this site? How do I know which table I need?

[Jeremy]

Yes, that's the right site. I believe you're interested in Covid19 in humans, so you can use the "Standard DNA codon table".