# Translating a eukaryotic FASTA file of CDS entries From DNA sequence to predicted protein is an example in [Biopython Cookbook "From gene sequence to predicted protein with the GFF module"](https://biopython.org/wiki/Gene_predictions_to_protein_sequences). Basing on DNA sequence and [GlimmerHMM](http://ccb.jhu.edu/software/glimmerhmm/) output in [GFF3](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format, the project script outputs protein coding sequences in fasta format. The project script and example input files are available from: Login and password will be distributed during class ``` ** install GFF module: pip install bcbio-gff ** Download reference DNA sequence file: ref.fa ** Download GlimmerHMM GFF3 output file: glimmer.gff ** Download project script: glimmergff_to_proteins.py ** run glimmergff_to_proteins.py with GFF3 file as the 1st argument and reference DNA file as the second argument ** The output protein sequence is a fasta file with the same suffix as the gff file and with the ending as proteins.fa ``` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://igb.mit.edu/mini-courses/python/biopython/example-projects/translating-a-eukaryotic-fasta-file-of-cds-entries.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.