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Information on the clone list representing a new 27K barley UniGene Set


Creators:

GabiPD Team, Bioinformatics, Max Planck Institute of Molecular Plant Physiology:
Birgit Kersten, Axel Nagel

Former RZPD:
Svenja Diehl

Institute of Plant Genetics and Crop Plant Research (IPK):
Patrick Schweitzer, Lothar Altschmied, Uwe Scholz, Nils Stein


Information on EST clustering:

459.231 public and IPK EST sequences were clustered using CAP3 and TGICL tools to get:
   • 27.729 ClusterContigs
   • 14.897 Cap3 Singlets
   • 26.956 TGICL Singlets.


Information on selection of sequences for the UniGene Set:

1. Selection of all CAP3 Singlet sequences from the EST clustering (1.266 sequences)

2. Selection of all TGICL Singlet sequences from the EST clustering (7.026 sequences)

3. Selection of one representative sequence from every ClusterContig by the following criteria (21.953 sequences):
    a) sequence overhang < 50%
    (sequence overhang is the part of the EST sequence which is not matching the
    consensus sequence of the ClusterContig)
    b) The sequence is matching the consensus sequence with at least 200 bp of its sequence.
    c) The sequence is matching the most 5-prime end of the consensus sequence.

⇒  List all distinct cDNA clones (UniClones) corresponding to the sequences selected in 1+2+3


Result:

List of 27.439 barley cDNA clones representing a new 27K UniGene Set enriched for full-length clones

  • Go to clone list



  • Links to other Barley EST assemblies:

  • HarvEST

  • GabiPD Webmaster