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lh3 / miniprot

Align proteins to genomes with splicing and frameshift
https://lh3.github.io/miniprot/
MIT License
310 stars 16 forks source link

Pgap 9185 gencode 1 #56

Closed azat-badretdin closed 4 months ago

azat-badretdin commented 4 months ago

The theme of this pull request - ability to run miniprot with more genetic codes, namely, in addition to "standard" ("1" in NCBI classification of gencodes), which matches in terms of stop codons and middle-of-the-sequence as popular prokaryotic code "11", the "Mold" genetic code ("4" in NCBI classification) - a lot of prokaryotic organisms use this code.

We found that using correct code "4" for these organism set produces improvements in annotation.

Thus - the nature of the request.

Thank you for your consideration!

lh3 commented 4 months ago

I have added -T to support NCBI translation table 1-5. Thanks for the PR anyway.

azat-badretdin commented 4 months ago

I have added -T to support NCBI translation table 1-5. Thanks for the PR anyway

Thank you very much, Heng! When do you think it will be released?

lh3 commented 4 months ago

Just released