Perhaps you could try
Tool: pinfish: tools to annotate genomes using long read transcriptomics data pinfish: tools to annotate genomes using long read transcriptomics data
and maybe also Transcriptome Annotation by Modular Algorithms (for Iso-Seq data) https://github.com/GenomeRIK/tama
This tool from EMBOSS might also be useful http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/getorf.html
Is this for genome annotation? If so, there are many resources for structural annotation of a genome on biostars to search for.