Nomenclature of exemplar sequences on the Barley1 GeneChip

    From Stacy Turner, Steve Wanamaker, Roger Wise and Timothy Close, 21 May 2003

    Barley1 GeneChip sequences designated as Controls, section 1,  
    section 2, or sections 3-11 have been named according to the 
    following format.
    
    In the Controls:
    The three reliably non-expressed barley sequences were named 
    according to their GenBank accession numbers and their position 
    within that sequence:
    
    >Barley1_AF427791.40321-46140
    >Barley1_AF427791.74797-75570
    >Barley1_AF427791.8829-9073
    
    In section 1:
    If a sequence existed in GenBank as a unique sequence, the GenBank 
    accession number was used as the name, such as Mla1: >Barley1_AY009939
    
    If a sequence existed in GenBank as part of a longer sequence, the 
    GenBank accession number was used, as well as something to identify 
    which part of that sequence was used.  There are two different 
    formats for this type, >Barley1_AF523679.53-147   and 
    >Barley1_AY196347.mRNA (.CDS was used in place of mRNA in one case).
    
    For the three sequences which currently do not exist in GenBank, they 
    were called:
    
    >Barley1_Mla_rtPCR_Franka
    >Barley1_Mla_rtPCR_Franka_b
    >Barley1_Mla_rtPCR_Kwan
    
    These products are named as such because they are rtPCR products 
    amplified using primers for Mla on the cultivars Franka and Kwan. 
    Two products were found in Franka, hence the Franka_b.
    
    In section 2: (non-barley reporter transgenes)
    Sequences are named with their GenBank name as they were in the two 
    different examples in section 1.
    
    In sections 3 - 11:
    Barley1 GeneChip sequences designated as sections 3 to 11 were 
    extracted using "output a unigene set" from HarvEST:Triticeae barley 
    assembly #25, with the "contigs and singletons" and "output consensus
    sequence" selections. Consistent with the nomenclature above, they have 
    been named according to the following format:
    
    >Barley1_##### where ##### is the HarvEST contig number.  Contig3 is 
    represented as >Barley1_00003.  Contig10037 is represented 
    as >Barley1_10037.