Table 3

Annotation statistics for ESTIMA:Songbird Build 3

Build 3

Percent total

20 K array subset

Percent of array

Percent of Build 3 category

Unique sequences after assembly

31658

100%

17214

100%

54%


    A) ALL HITS BY DATABASE

Gga Genome

21601

68%

12396

72%

57%

Chicken_TC

20208

64%

11715

68%

58%

Gga Unigene

17980

57%

10490

61%

58%

NCBI_Chicken_RNA

15904

50%

9110

53%

57%

Ensembl_Chicken_cdna_all

14609

46%

8348

48%

57%

Ensembl_Chicken_cdna_abinitio

13223

42%

7588

44%

57%

Chicken IPI

13219

42%

7898

46%

60%

Hs Unigene

12373

39%

7224

42%

58%

NCBI_Chicken_protein

7776

25%

4517

26%

58%


Hits against any database

24466

77%

13803

80%

56%


    B) Hierarchy of CUSTOM ANNOTATION

1 Use IPI-annotation*

13219

42%

7553

44%

57%

2 in GGA_Unigene but not IPI

5614

18%

3364

20%

60%

3 in HS but not IPI or GGA_unigene

265

1%

104

1%

39%


Total number of "custom annotations"

19098

60%

11021

64%

58%

4 additional "conserved in chicken"

5368

17%

2784

16%

52%


Hits against any database

24466

77%

13805

80%

56%

5 remainder = "TGU-specific" (no hits)

7192

23%

3409

20%

47%


31658

100%

17214

100%

54%


    *C) IPI Annotations

Number of sequences with IPI identifiers

13219

7898

(Unigene used for 345)

Number of unique IPI identifiers

8127

6035


All identifiers in IPI release 3.26

25500

25500

Fraction of total IPI identifiers

32%

24%


Replogle et al. BMC Genomics 2008 9:131   doi:10.1186/1471-2164-9-131

Open Data