Table 1

Re-annotation projects
What
 How
 Why
 New/Total
 %
 Who
 When
 Reference
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

Column names and explanations: What, species or chromosome; How, comments or methods; Why, the reasons for re-annotation - A, to find more genes; B, a cautionary statement; C, to find more functions; D, to achieve fewer errors; E, using new methods; F, to assess reproducibility; %, the improvement - in terms of additional genes predicted - over previous annotations, as a percentage of the total number of genes in the genome; Who, authors; When, publication year; Reference, citation. N/A denotes not applicable. * Denotes percentages that have not been taken into account for the calculation.

Ouzounis and Karp Genome Biology 2002 3:comment2001.1   doi:10.1186/gb-2002-3-2-comment2001