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Table 1 Re-annotation projects

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
  1. 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.