Changes between Version 47 and Version 48 of DescribingResidues


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Timestamp:
Aug 27, 2015, 2:11:36 PM (6 years ago)
Author:
mah79
Comment:

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  • DescribingResidues

    v47 v48  
    44== Describing amino acid residues for protein modifications etc ==
    55
    6  * Single Amino acid AA single letter code, residue number residue=K54 (residue=54 was used in legacy annotations but is now deprecated
    7  * Multiple single amino acid residues either residue=K54|residue=K22 or residue=K22,K54 as appropriate
    8  * Range of amino acids residue=A114-A660 (114-660 was used in legacy annotation but is now deprecated)
     6 * Single amino acid residue: AA single letter code, residue number, e.g. residue=K54 (legacy annotations that were missing the amino acid code have been corrected)
     7 * Multiple non-consecutive amino acid residues: either residue=K54|residue=K22 or residue=K22,K54 as appropriate (pipe for OR, comma for AND, as usual)
     8 * Range of amino acid residues: residue=A114-A660 (legacy annotations that were missing the amino acid code have been corrected)
    99 * Region not fully defined used residue=region_A114-A660
    10  * Special case i) in RNA pol II CTD domain residues tend to be referred to in context of the CTD domain and are annotated as CTD,S2|CTD,S5 (TODO FIX THESE)
    11  * Special case ii) Cleavage sites. Are defined as a range of 2 amino acids flanking the cleaved peptide bond, may not be the best way to do this...
    12   eg residue=R179-N180
     10 * Special cases
     11  * Phosphorylated residues in RNA polymerase II carboxy-terminal domain (CTD) repeats are specified relative to a canonical CTD repeat, rather than by position in the entire protein (it usually isn't feasible to tell how many repeats are actually phosphorylated on potential sites). They are annotated as residue=CTD_S2, residue=CTD_S5, etc.
     12  * Cleavage sites are defined as a range of 2 amino acids flanking the cleaved peptide bond, e.g. residue=R179-N180. (This may change someday, if we ever think of a better way to do it.)
    1313
    1414== Describing amino acid or nucleotide residues in allele descriptions ==