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Maize

Maize transposable element reference sequences, and genome annotation.


Analyses of genome sequence ZmB73_RefGen_v3 (Maize RefGen database V3 (release 5b.+) from Gramene.org).

The longest contigs were concatenated until the cumulative length was 300 Mbp. We used the TEdenovo pipeline (similarity and structural branches) with default parameters, and then annotate the initial sequence using the second TEannot process strategy to curate consensus by running a second TEannot only with consensuses that detect at least one copy aligned over more than 95% of the consensus.

All results are available here and obtained with REPET v2.4 . This archive contains:

  • ZmV3_consensusFLC_lib.fa : De novo library of consensus built on a 300Mbp genome subset.
  •  ZmV3_consensusFLC_lib.classif : classification information for each consensus of ZmV3_consensusFLC_lib.fa.
  •  chr*_ZmB73v3.gff3 : TEs annotation of each chromosome in gff3 format.
  •  ZmV3.globalAnnotStatsPerTE.txt : global annotation statistics for ZmB73_RefGen_v3 genome.

These data are under the creative commons copyright CC-BY.

Update: 21 Apr 2016
Creation date: 15 Apr 2016