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pauline-ng / SIFT4G_Create_Genomic_DB

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.jar to annotate VCF files.
GNU General Public License v3.0
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mitochondrial code #62

Closed pauline-ng closed 1 year ago

pauline-ng commented 1 year ago

By email from a user.

Hi, I was wondering if your program takes into consideration the differences in mitochondrial genetic code and genomic code in order to make predictions in mus musculus. Thanks,

pauline-ng commented 1 year ago

Yes, SIFT4G takes into account mitochondrial code.

We have a setting for mitochondrial genetic code when we build the SIFT4G predictions. Please see lines 4-5 h [github.com]here as an example.

Please use the SIFT4G predictions at this website: https://sift.bii.a-star.edu.sg/sift4g/ [sift.bii.a-star.edu.sg] for MT SNPs built with Mitochondrial genetic code.

pauline-ng commented 1 year ago

To clarify the same applies to the downloaded version or do I have to edit the code to get mito predictions in there?

pauline-ng commented 1 year ago

Use the download version --- the mito setting was set properly in the databases we built.