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Table 1 List of genomic data available in FLAGdb++

From: Exploration of plant genomes in the FLAGdb++ environment

Data type Feature number Sources
Arabidopsis thaliana   
AGI coding genes 28 094 TAIR [21, 39]
EuGène coding genes 27 981 * [19, 20]
RNA genes 1 288 TAIR [39] and miRbase [40]
Transposable elements 3 900 TAIR [39]
Curated repeat elements 31 876 * [36]
Transcript sequences (EST, cDNA) 1 281 393 GenBank, aligned with SIM4 [41]
Predicted smallRNA genes 609 * O. Voinnet et al. (unpublished data)
2 D structures 24 194 * Predicted by SOPMA, PHD, DSC [15]
3 D structures 8 492 * Predicted by Geno3 D [16]
Curated annotations 2 728 * [33, 34, 42]
Paralogs in duplicated segments 14 228 TIGR-JCVI [43]
FST 407 192 INRA, GABI, SAIL and SALK [44]
CATMA probes (GST and GFT) 35 283 * CATMA and CATdb [24, 25, 45]
Affymetrix micro-array probes 266 372 GeneChip® Arabidopsis ATH1
Chr. 4 tiling-array probes 21 752 * [26]
Whole genome tiling-array probes 1 434 492 * TAG project (unpublished data)
Promoter-array probes 11 904 * SAP project [27]
MPSS from mRNA and smallRNA 136 407 Arabidopsis MPSS plus [46, 47]
Gene families 3 500 PFAM profiles [32]
Protein motifs 38 631 PFAM profiles and HMMER [48]
Oryza sativa   
Coding genes 41 439 TIGR-JCVI and RAP-DB [49, 50]
RNA genes 718 TIGR-JCVI [49]
Repeat elements 16 185 TIGR-JCVI [49]
Transcript sequences (EST, cDNA) 1 120 229 GenBank, aligned with SIM4 [41]
Curated annotations 477 * [35]
FST 79 612 OryGenesDB [51]
Gene families 2 988 PFAM profiles [32]
Protein motifs 60 789 PFAM profiles and HMMER [48]
Populus trichocarpa   
Coding genes 45 555 JGI [10]
Repeat elements 29 366 JGI [10]
Transcript sequences (EST, cDNA) 322 996 GenBank, aligned with SIM4 [41]
Curated annotations 3 176 * J.-C. Leplé et al. (unpublished data)
Gene families 3 371 PFAM profiles [32]
Protein motifs 49 723 PFAM profiles and HMMER [48]
Vitis vinifera   
IGGP coding genes 26 347 Genoscope [11] using GAZE [52]
EuGène coding genes 44 414 * [19]
Repeat elements 336 729 Genoscope [11]
Transcript sequences (EST, cDNA) 419 542 GenBank, aligned with SIM4 [41]
Curated annotations 220 * TPS [22] and other unpublished families
Gene families 2 970 PFAM profiles [32]
Protein motifs 32 375 PFAM profiles and HMMER [48]
  1. *: original data, only in FLAGdb++