Anthony

Three-letter amino acid abbreviations

2

A low-priority issue, but it would be nice to eventually add the three-letter abbreviations for amino acids to the `aminoAcidValueMap` in `ProteinAlphabet`.

Mitochondrial genetic code variations

1

Bio.Algorithms.Translation.Codons contains the standard genetic code. Should there be a second codon map for mitochondrial genes? AGA and AGG are terminating codons in mitochondria, and UGA codes for tryptophan.

There's a check for GFF parsing that requires version 2. The parser works fine for version 3 (default version for Ensembl now), since the attributes are stored as free text....

VCF parser

2

Are you planning to integrate a VCF parser, or is there another parser I could use for VCF files? I see there's one in development over on this repository: https://github.com/evolvedmicrobe/Bio.VCF....

Suffix arrays for alignment

2

This is a wonderful library of functions for bioinformatic analysis. I'm excited to try it out! Do you have any plans to implement an alignment algorithm similar to [STAR](https://github.com/alexdobin/STAR), which...

It'd be nice to have a wizard for creating new proteases on this page: Here's a description of an example problem and a workaround in the meantime. https://github.com/smith-chem-wisc/MetaMorpheus/issues/2041 

Switching MetaMorpheus and mzLib from AppVeyor/Jenkins to GitHub Actions?

10

I've recently switched Spritz and TopDownSDK over from using AppVeyor to using GitHub Actions for continuous builds and periodic testing, and I'm finding it to be pretty great in comparison....

Restructure base directory

4

https://github.com/smith-chem-wisc/MetaMorpheus/issues/1956

Commandline improvements

10

- [x] Dockerize it - [x] Make smithchemwisc Docker account - [x] Automatic builds of docker image from the release branch on Docker Hub - [x] Update readme for .NET...