PERFORMANCE OF FTGPRED ALGORITHMS ON GENEs/ORFs MISSED BY DIFFERENT GENE PREDICTORS.:
False Negatives are those ORFs/Genes for which the program fails to predict at least one end correctly. Only experimentally confirmed ORFs or Genes from the GenBank annotation (that were neither hypothetical nor putative) were taken as true ORFs.
GeneMarkS:
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ORGANISM | FALSE NEGATIVES |NO. OF MISSED ORFs/GENEs DETECTED BY|
| |-------------------------------------
| | FTG | GENESCAN | L-S* |
-----------------------------------------------------------------------------------
A. pernix | 12 | 10 | 10 | 5 |
B. anthracis str Ames | 28 | 27 | 15 | 13 |
B. burgdorferi | 36 | 36 | 9 | 14 |
C. pneumoniae AR39 | 4 | 4 | 3 | 2 |
C. jejuni | 7 | 6 | 2 | 2 |
E. coli | 228 | 218 | 173 | 146 |
H. influenzae Rd | 4 | 4 | 4 | 3 |
H. pylori 26695 | 8 | 6 | 4 | 4 |
H. pylori J99 | 6 | 6 | 2 | 2 |
M. tuberculosis O157:H7 | 27 | 25 | 23 | 20 |
M. genitalium | 45 | 45 | 41 | 41 |
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*L-S: Lengthen-Shuffle Algorithm
GeneMark.hmm:
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ORGANISM | FALSE NEGATIVES |NO. OF MISSED ORFs/GENEs DETECTED BY|
| |-------------------------------------
| | FTG | GENESCAN | L-S* |
-----------------------------------------------------------------------------------
A. pernix | 7 | 6 | 7 | 3 |
B. anthracis str Ames | -- | -- | -- | -- |
B. burgdorferi | 36 | 36 | 8 | 13 |
C. pneumoniae AR39 | 9 | 8 | 5 | 5 |
C. jejuni | 7 | 7 | 6 | 5 |
E. coli | -- | -- | -- | -- |
H. influenzae Rd | 4 | 4 | 2 | 2 |
H. pylori 26695 | 7 | 5 | 4 | 3 |
H. pylori J99 | 6 | 6 | 4 | 3 |
M. tuberculosis O157:H7 | 28 | 27 | 25 | 22 |
M. genitalium | 273 | 270 | 264 | 248 |
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*L-S: Lengthen-Shuffle Algorithm
EasyGene 1.0:
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ORGANISM | FALSE NEGATIVES |NO. OF MISSED ORFs/GENEs DETECTED BY|
| |-------------------------------------
| | FTG | GENESCAN | L-S* |
-----------------------------------------------------------------------------------
A. pernix | 10 | 10 | 8 | 4 |
B. anthracis str Ames | 37 | 35 | 23 | 18 |
B. burgdorferi | 43 | 43 | 10 | 17 |
C. pneumoniae AR39 | 9 | 9 | 7 | 4 |
C. jejuni | 24 | 23 | 14 | 13 |
E. coli | 1748 | 1727 | 1677 | 1579 |
H. influenzae Rd | 4 | 4 | 1 | 1 |
H. pylori 26695 | 9 | 7 | 4 | 5 |
H. pylori J99 | 6 | 6 | 2 | 2 |
M. tuberculosis O157:H7 | 35 | 33 | 31 | 28 |
M. genitalium | 6 | 6 | 3 | 4 |
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*L-S: Lengthen-Shuffle Algorithm
Glimmer:
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ORGANISM | FALSE NEGATIVES |NO. OF MISSED ORFs/GENEs DETECTED BY|
| |-------------------------------------
| | FTG | GENESCAN | L-S* |
-----------------------------------------------------------------------------------
A. pernix | 4 | 4 | 3 | 1 |
B. anthracis str Ames | 36 | 34 | 21 | 19 |
B. burgdorferi | 27 | 27 | 7 | 11 |
C. pneumoniae AR39 | 9 | 9 | 7 | 5 |
C. jejuni | 9 | 9 | 4 | 4 |
E. coli | 109 | 105 | 65 | 56 |
H. influenzae Rd | 2 | 2 | 1 | 0 |
H. pylori 26695 | 10 | 9 | 7 | 5 |
H. pylori J99 | 8 | 8 | 5 | 4 |
M. tuberculosis O157:H7 | 19 | 18 | 18 | 14 |
M. genitalium | 45 | 45 | 43 | 41 |
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*L-S: Lengthen-Shuffle Algorithm