compare genome to find out unique(s) gene

Question

[microorganism_001]

How to find species-specific genes from a genome, compare two genomes, and find out particular genes available to one genome and not to another. please tell me about any tool/ r-package/ resources that will help me. Thanks.

Answer 1

[mboutrou]

I think you are looking for pangenome tools life panaroo (https://github.com/gtonkinhill/panaroo) or PanACoTA (https://github.com/gem-pasteur/PanACoTA). It will give you a list of all the genes present in the genomes, specifying for each one the list of genomes where it is present. You cannot run them in R though you have to use the command-line.

[microorganism_001]

I have gone through about two tools but have not gotten the answer to my question. Thanks.

[mboutrou]

Are you not looking for something like the gene_presence_absence.csv of panaroo? (https://gtonkinhill.github.io/panaroo/#/gettingstarted/output). Also in R pagoo package seems to be good to analyze the pangenomes after panaroo (or any other pangenome tool) (https://cran.r-project.org/web/packages/pagoo/pagoo.pdf)

[microorganism_001]

Thank you mboutrou for your informative response, I am using panaroo tool and with the following command getting the error tell me how can I fix this? -

(panaroo) omic@omics-world-001:~/Pictures/unique_gene/panaroo$ panaroo -i *.gff -o ./results/ --clean-mode strict -f 0.5
/home/omic/miniforge3/envs/panaroo/lib/python3.9/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
  warnings.warn(
pre-processing gff3 files...
  0%|                                                                                                  | 0/2 [00:00<?, ?it/s]Problem reading GFF3 file:  genomic_KSK1.gff
  0%|                                                                                                  | 0/2 [00:00<?, ?it/s]
Error reading prokka input!
Traceback (most recent call last):
  File "/home/omic/miniforge3/envs/panaroo/lib/python3.9/site-packages/panaroo/prokka.py", line 294, in process_prokka_input
    gene_sequence_list = Parallel(n_jobs=n_cpu)(
  File "/home/omic/miniforge3/envs/panaroo/lib/python3.9/site-packages/joblib/parallel.py", line 1863, in __call__
    return output if self.return_generator else list(output)
  File "/home/omic/miniforge3/envs/panaroo/lib/python3.9/site-packages/joblib/parallel.py", line 1792, in _get_sequential_output
    res = func(*args, **kwargs)
  File "/home/omic/miniforge3/envs/panaroo/lib/python3.9/site-packages/panaroo/prokka.py", line 143, in get_gene_sequences
    raise RuntimeError("Error reading prokka input!")
RuntimeError: Error reading prokka input!

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/omic/miniforge3/envs/panaroo/bin/panaroo", line 10, in <module>
    sys.exit(main())
  File "/home/omic/miniforge3/envs/panaroo/lib/python3.9/site-packages/panaroo/__main__.py", line 314, in main
    process_prokka_input(args.input_files, args.output_dir,
  File "/home/omic/miniforge3/envs/panaroo/lib/python3.9/site-packages/panaroo/prokka.py", line 306, in process_prokka_input
    raise RuntimeError("Error reading prokka input!")
RuntimeError: Error reading prokka input!