What's the best practice for locating a gene in SPAdes assembly graph?

[nettanetta]

Hi!
I have a set of gene sequences (given in amino acids), and I'd like to locate their corresponding nucleotide sequences in the assembly graph. My desired input for each query gene is a corresponding path in the graph, a starting point in the first node of this path and an ending point in the last node of this path.
So far, I searched for the genes in the "contigs.fasta" file using MMseqs2 and then I generated the desired output myself based on the contigs.path file. However, this didn't work in case that there are gaps in the paths corresponding to assembly contigs.

• Is there a best practice for doing this?
• Is there a recommended tool for searching for protein sequences in the SPAdes assembly graph? I read about SPAligner But although the paper describes the alignment of protein sequences, There is no such option according to the documentation.
• Is there a way to reverse engineer the gaps and use the alignment of genes to the assembly contigs to locate the genes in the assembly graph?

thank you!
Netta