I have a fasta file with a set of about 300 contigs. What I would like to do is find some sort of gene annotation/prediction software, so I can identify any genes of known function that might be present in my fasta file (based on known genes in other eukaryotes). I tried using maker, but had some problems which I think may be linked to the fact that the contig set is so small (e.g. it is not a eukaryotic assembly).

Is there any stand-alone gene prediction software out there that might be suitable for a small data set like this?

Ultimately I am just trying to figure out if I can link any of these sequences back to genes with known functions.