Changes between Version 46 and Version 47 of DescribingResidues


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Timestamp:
Apr 10, 2015, 3:11:22 PM (6 years ago)
Author:
mah79
Comment:

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  • DescribingResidues

    v46 v47  
    22= Describing Residues Modified or Mutated =
    33
    4 == Describing Amino Acid Residues for Modifications etc ==
     4== Describing amino acid residues for protein modifications etc ==
    55
    66 * Single Amino acid AA single letter code, residue number residue=K54 (residue=54 was used in legacy annotations but is now deprecated
     
    1212  eg residue=R179-N180
    1313
    14 == Describing Amino Acid Residues and Bases to for allele descriptions ==
     14== Describing amino acid or nucleotide residues in allele descriptions ==
    1515
    16 === Amino Acids ===
    17  * Mutation of amino acids to specific stop codons (i.e important if generating read-through)
    18    allele=name(W234->opal)
    19  * Mutation of single amino acid residue: allele=name(K132A)
    20  * Mutation of multiple single AA residues (not consecutive): allele=name(K132A,K144A)
    21  * Mutation of multiple consecutive AA residues: range in single letter code, number of first AA  in range, range of residues mutated to e.g. allele=Rhp54Km(KEN26AAA);
    22  * Legacy data (In Artemis) all allele data in Artemis which is not in the form allele=name(description) is ALL in the form allele=name ONLY e.g. allele=htbK119R
    23  * Partial AA deletion: allele=name(del_100-200) for proteins
     16=== Amino acids ===
     17Choose the allele type from the Canto pulldown
     18 * Mutation of single amino acid residue: K132A
     19 * Mutation of multiple amino acid residues
     20  * not consecutive: comma separate, e.g. K132A,K144A
     21  * consecutive: wild-type sequence in single letter code, number of first position in range, mutated sequence, e.g. KEN26AAA
     22 * Partial deletion: indicate the positions of the deleted residues, e.g. 100-200
    2423 * Note that for almost all proteins, amino acid numbering is based on the '''unmodified''' protein. The annoying exception is histones, which are numbered assuming removal of the initiator methionine.
    25  * Allele=heterozygous for heterozygous diploid? (check at next inhouse meeting)
     24 * Nonsense mutation (i.e. mutation of an amino acid to a stop codon)  * specific stop codons: W234->opal, W234->amber, W234->ochre
     25  * without specifying which stop codon: W234->stop
     26 * Note that for almost all proteins, amino acid numbering is based on the '''unmodified''' protein. The annoying exception is histones, which are numbered assuming removal of the initiator methionine.
     27 * Legacy data (Artemis): all allele data in Artemis which is not in the form allele=name(description) is ALL in the form allele=name ONLY e.g. allele=htbK119R
    2628
    27 
    28 === Bases ===
    29  * No examples yet curated; if any needed, follow patterns as for amino acids, but include 'nt' to indicate nucleotides, e.g.
    30   * single changes: ntA25G
    31   * partial deletions: delnt_100-200
    32  * Note that if neither 'aa' nor 'nt' is included, 'aa' (amino acids) will be assumed
     29=== Nucleotides ===
     30 * Select the appropriate "... nucleotide ..." allele type in Canto
     31 * Follow patterns as for amino acids, e.g.
     32  * single changes: A25G
     33  * multiple consecutive changes: AG25TT
     34  * multiple non-consecutive changes: A25T,G35T
     35  * partial deletions: 100-200
     36 * Number starting from the first nucleotide of the coding sequence, i.e. position 1 is the A of the initiator ATG. Use negative numbers for positions upstream of the ATG.
    3337
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