Table 4.
Performances of assembly programs with a curated Arabidopsis EST dataset (minimum overlap: 40 bp, minimum overlap percent identity: 97%, maximum overhang: 10 bp)
| iAssembler | CAP3 | MIRA | TGICL | Phrap | Newbler | |
|---|---|---|---|---|---|---|
| No. unigenes | 39,357 | 71,082 | 81,042 | 40567 | 70,364 | 41,930 |
| Average unigene length (bp) | 513.1 | 405.8 | 338.0 | 499.3 | 340.8 | 481.8 |
| No. unigenes perfectly aligned to Arabidopsis cDNAs* | 38,907 | 70,870 | 80,669 | 40,176 | 69,105 | 41,231 |
| No. unigenes not perfectly aligned to Arabidopsis cDNAs | 450 | 212 | 373 | 391 | 1,259 | 699 |
| No. unigene pairs perfectly aligned to same Arabidopsis cDNAs with > = 40 bp overlaps (type II error) | 465 | 28,630 | 41,696 | 1,729 | 34,735 | 4,587 |
| No. ESTs and corresponding unigenes not aligned to same Arabidopsis cDNAs (type I error) | 158 | 83 | 173 | 1,022 | 4,283 | 2,753 |
*perfectly aligned means that the sequences were aligned to Arabidopsis cDNAs in their entire lengths