Table 1 Re-annotation projects

Yeast chromosome III

The very first re-annotation; 17 new predictions compared to the original 57 (74 total assignments)

C, E

17/182

9.3

Bork et al.

1992

[20,21]

Yeast chromosome III

Subsequent re-annotation; 19 predictions over the 74 above (93 total assignments)

C

19/171

11.1

Koonin et al.

1994

[22]

Various archaeal species

One of the first large-scale analyses, but not genome-wide

E

30/95

31.6^*

Ouzounis et al.

1995

[1]

Yeast chromosome VIII

Re-annotation

C

24/269

8.9

Ouzounis et al.

1995

[24]

Haemophilus influenzae

Automated genome annotation; 148 new assignments over previous 1,007 (1,155 total assignments)

C, E

148/1,743

8.5

Casari et al.

1995

[9]

Haemophilus influenzae

Additional gene findings

A

17/1,743

0.1

Robison et al.

1996

[10]

Haemophilus influenzae

Re-annotation and metabolic reconstruction; 1,408 total assignments (cf. 1,155 above)

E

253/1,703

14.9

Tatusov et al.

1996

[8]

Haemophilus influenzae

Metabolic reconstruction

E

Individual cases

N/A

Karp et al.

1996

[7]

Mycoplasma genitalium

Additional gene findings

A

3/470

0.6

Robison et al.

1996

[10]

Mycoplasma genitalium

Re-annotation

C

21/470

4.5

Ouzounis et al.

1996

[11]

Methanococcus jannaschii

Manual re-annotation

C

214/1,738

12.3

Kyrpides et al.

1996

[14]

Methanococcus jannaschii

Re-annotation; reproducibility study

C, F

23/1,682

1.4

Andrade et al.

1997

[13]

Saccharomyces cerevisiae

Short open reading frame identification

A

10/6,357

0.2

Andrade et al.

1997

[23]

Various species

Cautionary statement

B

Individual cases

N/A

Smith and Zhang

1997

[3]

Methanococcus jannaschii

Cautionary statement

B

Individual cases

N/A

Kyrpides and Ouzounis

1998

[34]

Methanococcus jannaschii

Cautionary statement

B, D

20/1,738

1.2

Kyrpides and Ouzounis

1999

[15]

Chlamydia trachomatis

Cautionary statement

B, D

10/893

1.1

Kyrpides and Ouzounis

1999

[15]

Campylobacter jejuni

Cautionary statement

B

Individual cases

N/A

Pallen et al.

1999

[27]

Methanococcus jannaschii

Additional gene findings

A

31/1,773

1.8^*

Raghavan and Ouzounis

1999

[17]

Methanobacterium thermoautotrophicum

Additional gene findings

A

13/1,871

0.7^*

Raghavan and Ouzounis

1999

[17]

Archaeoglobus fulgidus

Additional gene findings

A

27/2,409

1.1^*

Raghavan and Ouzounis

1999

[17]

Pyrococcus horikoshii

Additional gene findings

A

42/2,061

2.0^*

Raghavan and Ouzounis

1999

[17]

Plasmodium falciparum chromosome II

Re-annotation; reproducibility study

F

21/210

10.0

Tsoka et al.

1999

[25]

Mycoplasma genitalium

Comparison of other annotations, reproducibility study

F

Individual cases

N/A

Brenner

1999

[33]

Aeropyrum pernix

COGs matching

E

315/2,694

11.7

Natale et al.

2000

[26]

Pyrococcus abyssii

COGs matching

E

Individual cases

N/A

Natale et al.

2000

[26]

Mycoplasma genitalium

Contextual analysis

E

21/480

4.4

Huynen et al.

2000

[12]

Mycoplasma pneumoniae

Contextual analysis plus experiments

E

109/688

15.8

Dandekar et al.

2000

[18]

Thermotoga maritima

Contextual analysis

E

193/1,877

10.3

Kyrpides et al.

2000

[19]

In total: 10+ species

Key result: 7 ± 5% ( ^* excluded)

Approximately ten groups

Nine years

23 papers