Table 1

Summary of Enhanced Organismal Databases Searchable by RAId_DbS

Organism

DB_name

Protein

NP

NM

SP

SAPs

PTMs

DB_size (byte)


Homo sapiens

hsa

29284

35059

35031

15030

116073

84406

16,265,018

Anopheles gambiae

angam

12388

12719

12706

112

350

50

6,042,277

Arabidopsis thaliana

artha

29651

31740

31711

5527

5207

11977

12,318,213

Bos taurus

botau

23796

26504

26491

3979

3295

15810

11,188,490

Caenorhabditis elegans

caele

22563

23097

23097

2890

1045

7756

10,050,609

Canis familiaris

cafam

31705

33834

33821

528

2766

4196

18,458,474

Danio rerio

darer

31192

36150

36137

1552

7358

3841

14,477,794

Drosophila melanogaster

drmel

17232

20207

20207

2568

5611

9290

9,796,785

Equus caballus

eqcab

17300

17637

17624

171

485

1045

9,404,150

Gallus gallus

gagal

18154

18724

18681

1455

1109

6522

8,728,501

Macaca mulatta

mamul

32547

38141

38128

207

1370

1262

14,498,187

Mus musculus

mumus

28506

35503

35451

12170

27614

61684

14,363,491

Oryza sativa

orsat

26636

26784

26777

1205

1291

2182

10,679,924

Pan troglodytes

patro

41464

52130

52117

482

3721

3734

20,217,986

Plasmodium falciparum

plfal

5240

5267

5267

88

56

184

3,995,386

Rattus norvegicus

ranor

28914

39425

39389

5569

9297

33240

15,879,569

Saccharomyces cerevisiae

sacer

5699

5880

0

5807

5507

13220

2,927,330


The header abbreviations in this table are explained as follows. The second column, headed by DB_name, documents the abbreviated database name for searches using standalone version of RAId_DbS. The column headed by "Protein" indicates the final number of protein clusters in the processed organismal databases. The columns headed by NP, NM, and SP summarize the breakdown of the total number of accession numbers included respectively from protein products, transcript products, and SwissProt protein entries. The columns headed by SAPs and PTMs indicate respectively the total number of annotated SAPs and PTMs included. The last column shows the database size in bytes.

Alves et al. BMC Genomics 2008 9:505   doi:10.1186/1471-2164-9-505

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