Two different genomes in a single fasta file

[Nikunj Maheshwari]

Hi,

I have two different genomes (G1 and G2) in two separate files. When I run Prodigal on them separately, I get x and y number of proteins respectively. When I concatenate the two fasta files into a single fasta file (with two different IDs, of course) and run Prodigal again, I get x1 and y1 number of proteins for G1 and G2 respectively, which is not the same as x and y. Is there a reason behind this? Could it be that Prodigal considers a single genome in the single file and trains on it? I might be missing something very basic here, but I am new to Prodigal, so I wouldn't know.
Any help would be greatly appreciated.

Thanks.

[Doug Hyatt]

Prodigal treats the contents of a FASTA file as a single genome.  You should split your genomes into separate files.  You can also analyze using metagenomic mode (-p meta), but this is not recommended for large sequences.

From the wiki ( https://github.com/hyattpd/prodigal/wiki/advice-by-input-type ):

TIP: Never analyze a multiple FASTA file containing sequences from more than one genome using normal mode. The only exception to this rule would be if the genomes are closely related (strains of the same species).

--
You received this message because you are subscribed to the Google Groups "prodigal-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to prodigal-discu...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.