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 sequence was performed on the predicted a.a. sequences, and it returned a list of sequences (hits) that are below an E-value threshold. Now I'd like to get the nucleotide sequences of the hits from hmmsearch, is there any software that can achieve this?
Thank you very much!
Due to the degeneracy of the genetic code, you cannot just back-translate the sequence. Whether you can directly retrieve the nucleotide sequences of your hits depends on whether the protein sequence database you used contain links to the original nucleotide sequence or not.
Try using TBLASTN which compares a protein query to a DNA database, in the 6 possible frames of the database.
Thank you, Dr.Annemarie Honegger and Dr.Vipul Batra for your great answers!
I have just found a solution to achieve that. It would require me to add a -d genes.fna flag in addition to -a proteins.faa when running Prodigal. Because the two files would contain identical headers, thus nucleotide seqs and protein seqs can be matched and recovered this way.
Hi Rui Zhang I am also interested in this method. Could you share the software
I assume it is this one:
Prodigal (PROkaryotic DynamIc programming Genefinding ALgorithm) is an open source lightweight microbial genefinding program developed at University of Tennessee and Oak Ridge National Laboratory. https://github.com/hyattpd/Prodigal
Article Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser ...
https://www.biostars.org/p/52583/
Hi Nguyen Tien Cuong , sorry I missed your earlier comments. Yes, as Annemarie Honegger has mentioned, the tool is called Prodigal. But to identify the target protein of your interest, you would have to first build a profile HMM and search your protein sequences with it using the hmmsearch function from the HMMER software.
Hope it helps.
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