Gene prediction programs that work with multi-fasta files

[Hobbe]

We have a draft genome of a fungus with around 4000 contigs. I have been using Genemark-ES on the multiple contig fasta file, but it finds genes that stretches over two contigs, and thus do not exist.

Are there gene finder programs (for eukaryotes) that work with multiple contig fasta files, or do I need to split my file into single contig files? Sounds like a real mess when you have over 4000 contigs...

Thanks,
Henrik