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Relatively easy to re-implement

• [multiple gff lines of intra-model] Redundant gene length (Ema0001)
• [multiple gff lines of intra-model] Internal stops in amino acid sequence (Ema0002)
• [multiple gff lines of intra-model] child feature not within parent boundaries (Ema0003)
• [multiple gff lines of intra-model] Incomplete gene feature (Ema0004)
• [multiple gff lines of intra-model] pseudogene has unusual child features, such as mRNA (Ema0005)

Translator method in the current version of gff3_to_fasta (v0.0.1) only considers standard codons and universal stop codons for generating peptide sequences. However, the genetic codes used for translation might be different for different species. Therefore, as suggested by @childers, it will be great if the translator method in this program can further consider to incorporate multiple codon tables for multiple species.

NCBI has compiled related information for codon tables for different species on April 30, 2013 (The Genetic Codes). These suggested codon tables can be incorporated into this program in the future.

Before this program incorporated this improvement, a list of other translation tools is suggested for users: http://molbiol-tools.ca/Translation.htm

Two tools with translation function having options for choosing genetic codes are recommended:

• ExPASy – Translate tool (ExPASy, University of Geneva, Switzerland). This site useful if users have a gene which begins with an alternative start codon.
• Translate Nucleic Acid Sequence Tool (University of Massachusetts Medical School, U.S.A.) which permits choice of reading frame(s) and genetic code.

Relatively hard to re-implement

• [multiple gff lines of inter-models] Duplicate transcripts/exon/CDS (Emr0001)
• [multiple gff lines of inter-models] merged gene parent (Emr0002)
• [multiple gff lines of inter-models] split gene parent (Emr0003)
• [multiple gff lines of inter-models] distant isoforms (Emr0004)

Relatively easy to re-implement

• [Single gff line] Negative or 0-based coordinates (Esf0002)
• [Single gff line] gene/mRNA that should be pseudogene (Esf0001)
• mRNA/transcript model without strand information (Esf0003)