Convert gene sequence into protein sequence them HMM

Question

[robert.murphy]

I want to take a gene sequence and identify if a metagenomic dataset posess this gene. I figured the best way to do this would be converting the gene sequence into a protein sequence and then into a HMM and using hmmsearch to look in the metagenomeic dataset.

Firstly, is this a good approach?

Secondly if it is, how do I do this?

Thank you for any advice!

Answer 1

[Fatima]

I believe HMM is a good fit for looking into protein families.

For a gene of interest and a meta-gnome I'd take one of these approaches:

1) using blastn to aligning the gene sequence to the meta-genome

2) using blastx or a gene sequence to protein sequence convertor (script or server) to find the protein sequence of the gene sequence and aligning it (tblastn) to the meta-genome.

3) using a tool like Fraggenescan to predict the genes in the meta-genome and would aligning the gene sequence to the output (Fraggenscan outputs gene sequence, protein sequence, ...)

4) using blastx or a gene sequence to protein sequence convertor to find the protein sequence of the gene sequence and aligning it (blastp) to the protein sequences in the meta-genome.

https://omics.informatics.indiana.edu/FragGeneScan/