Table 1.
Glimmer3 and Glimmer2 long-orfs output comparison
| Genome |
Glimmer3 long-orfs |
Glimmer2 long-orfs |
G3 versus G2 |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Organism | GC% | # Genes | 3′ Matches | Extra | 3′ Matches | Extra | 3′ Matches | Extra | |||
| A.fulgidus | 49 | 2398 | 1083 | 45% | 26 | 706 | 29% | 18 | +377 | +16% | +8 |
| B.anthracis | 35 | 5308 | 3494 | 66% | 194 | 2934 | 55% | 160 | +560 | +11% | +34 |
| B.subtilis | 44 | 4095 | 2647 | 65% | 21 | 2062 | 50% | 21 | +585 | +14% | 0 |
| C.tepidum | 57 | 2252 | 943 | 42% | 37 | 438 | 19% | 30 | +505 | +22% | +7 |
| C.perfringens | 29 | 2660 | 2111 | 79% | 16 | 1885 | 71% | 16 | +226 | +8% | 0 |
| E.coli | 51 | 4231 | 2754 | 65% | 39 | 1815 | 43% | 17 | +939 | +22% | +22 |
| G.sulfurreducens | 61 | 3438 | 1432 | 42% | 59 | 553 | 16% | 61 | +879 | +26% | −2 |
| H.pylori | 39 | 1556 | 1141 | 73% | 20 | 831 | 53% | 10 | +310 | +20% | +10 |
| P.fluorescens | 63 | 6134 | 2873 | 47% | 71 | 579 | 9% | 129 | +2294 | +37% | −58 |
| R.solanacearum | 67 | 3435 | 1133 | 33% | 42 | 157 | 5% | 131 | +976 | +28% | −89 |
| S.epidermidis | 32 | 2487 | 1797 | 72% | 40 | 1480 | 60% | 27 | +317 | +13% | +13 |
| T.pallidum | 53 | 1034 | 507 | 49% | 7 | 379 | 37% | 6 | +128 | +12% | +1 |
| U.parvum | 26 | 614 | 400 | 65% | 0 | 338 | 55% | 9 | +62 | +10% | −9 |
| Averages: | 57% | 39% | +628 | +18% | −5 | ||||||
For each genome, ‘#Genes’ counts all genes longer than 90bp in the NCBI annotation after removing genes with frame shifts and internal stop codons. A prediction is a match iff it has the same reading frame and stop codon as a gene. Extra predictions are those that are not matches. The ‘G3 versus G2’ column is the Glimmer3 value minus the Glimmer2 value.