How can I retrieve nucleotide sequences from amino acid sequences?

Question

[Rui]

Hello everyone,

Here is my situation. I have some nucleotide sequences from which amino acid sequences were predicted using Prodigal. Then an hmmsearch of a target amino acid seqs was performed on the predicted a.a. seqs, and it returned a list of hits that are below an E-value threshold. Now I'd like to get the nucleotide seqs of the hits from hmmsearch, is there any software that can achieve this?

Thank you very much!

[lieven.sterck]

as said here before, without prior knowledge it is not possible to get the nucleotide sequence from a given protein sequence.

However, if the protein sequences you screened with the hmmsearch is against a DB of known proteins (eg. from the human genome) you can perhaps back-trace the nucleotide sequence based on the protein IDs.

[Rui]

Thank you for your answer Lieven, do you have any idea what tool should I use to back-trace the nucleotide sequences?

[lieven.sterck]

no tool required, I was thinking along the line of looking up the IDs in the DBs.

Answer 1

[Mensur Dlakic]

There is no way to recover the exact nucleotide sequence from proteins due to genetic code degeneracy.

When you run prodigal, simply use both -a proteins.faa and -d genes.fna switches. That way you will have both protein and DNA sequences.

[Rui]

Thank you Mensur, this is great, I am gonna give it a try!

I also wonder if it's possible to match the protein hits returned from hmmsearch to the sequences in genes.fna?

[Rui]

Hello Mensur, so I just re-ran prodigal by including the -d option, the header sections are identical as that of the protein sequences created from the -a option. This way I will be able to match the protein seq with the DNA seq.

Thank you for your great solution, I appreciate it!