How to find genes that do not have any homologous in the OrthoMCL output?

Question

[2351688559]

Hi!

Is there anyone using the OrthoMCL programs?

Recently, I met a problem, that is, I could not find the genome-specific genes that do not have any homologous(even paralogous) in the final output file of OrthoMCL.

I think those genes are of great importance and should not be ignored in the comparative genomic analysis.

I really want to find them out, but I don't have any idea how.

Many thanks!

[Antonio R. Franco]

What databases have you used?

[2351688559]

MySQL, as proposed by the user guide.

Answer 1

[5heikki]

For example with pyfasta:

pyfasta extract -help
Usage: extract some sequences from a fasta file. e.g.:
               pyfasta extract --fasta some.fasta --header at2g26540 at3g45640

Options:
  -h, --help     show this help message and exit
  --fasta=FASTA  path to the fasta file
  --header       include headers
  --exclude      extract all sequences EXCEPT those listed
  --file         if this flag is used, the sequences to extract are read from
                 the file specified in args
  --space        use the fasta identifier only up to the space as the key