Frequently_Asked_Questions

Frequently Asked Questions (FAQ)

• A missense variant can impact more than one transcript of a gene. Which transcript should I use?

  • Phytozome provides a single gzipped file that identifies primary transcripts. Assuming the primary transcript is the most frequently expressed version of the gene, it is reasonable to focus on this transcript. Sequence conservation is calculated on a per codon basis and is not expected to vary dramatically among transcripts.

• Can a deleterious variant occur in some transcripts and not others?

  • This isn't common, but exon skipping, for example, could cause a variant to be present in some transcripts but not others.

• How do I convert a Variant Effect Predictor (VeP) report into the input format for BAD_Mutations?

  • The supporting script VEP_to_Subs.py does the conversion.

• Can I use BAD_Mutations to annotate deleterious variants in Iberian frogs?

  • Currently, BAD_Mutations is configured to work with angiosperms (seed plants). The fetch function in BAD_Mutations retrieves genome sequences from standardized sources. Currently, this includes Phytozome, which is plant-specific, and Ensembl Plants. Ensembl provides genomes for many species, but "handlers" configured to download these species would need to be written.

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