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I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain disulfide bridges within class I a1 domain). To do this I need to align the peptide sequences of transcripts of that model organism with transcripts of classical MHC I human genes and see which genes from those transcripts have those structural features. So I am looking for a tool to align and annotate those structural features in a replicable manner

Additionally if you have any other bioinformatic ideas /computational analyses on how to find classical MHC Class I molecules on an organism which is poorly annotated that would highly appreciated!

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  • $\begingroup$ Check out bioinf.jku.at/software/msa You can do the alignment in R and annotate there in a very replicable manner once you learn the package. You can also align it in Clustal Omega (use the protein option to align), or unitprot.org/align $\endgroup$
    – m4rio
    May 11 at 18:22

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