How to detect specific genes in metagenomics data

Question

[aziznasr1920]

Hello,

I have some shotgun metagenomics data (long reads sequenced by ONT).

I want to use those metagenomics data in order to detect the presence of a specific gene (Cyp51) or its mutated homologous.

I am a little bit confused because I had many ideas in my mind: write a Python code to detect the gene with a certain threshold of similarity, using classifiers like Kraken2 with a specific database containing the ref seq of the gene, BLAST, assembly then annotation, or just use specific tools (I didn't find the one until now)

Anyway, I wanna hear to ur opinions. if you were in my place, what is the strategy and tools that you would work with? Are there specific tools or pipelines that I can use directly, or anything that can help me?

Thanks in advance.

Have a good day

Answer 1

[Decimus Maximus]

There are a few ways to approach this. One would be Sequence Alignment or Sequence Similarity Search (using tools like BLAST or HMMER, you could perform a sequence similarity search to identify reads that match your gene of interest). Read Classification (using a tool like Kraken2), you could classify your reads based on a database of reference sequences. Metagenome Assembly and Annotation, this approach would involve assembling your metagenomic reads into larger contigs and then annotating those contigs to identify genes of interest. There are various tools available for metagenome assembly (MEGAHIT or metaSPAdes) and annotation (Prokka or EggNOG-mapper). You can write your own Python code and utilise e.g., Biopython to handle the DNA sequences and perform tasks like sequence alignment. Lastly, you can use gene-specific analysis and since you are working with Cyp51 and its homologs, you might also consider a database called CYPED dedicated to cytochrome P450 enzymes.

Good luck

[ATpoint]

I am tempted to ask since this and your previous answers have striking similarity to its general way of answering and tone: Is this your answer of ChatGPT? AI-derived answers should be indicated as such since they're not based on your own knowledge. Can you please clarify? Apologies if I am wrong.