From: The past, present and future of genome-wide re-annotation
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 |