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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 (unpublished data)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TAG project (unpublished data)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 (unpublished data)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TPS [22] and other unpublished families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++