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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)

From: iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences

 

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

  1. *perfectly aligned means that the sequences were aligned to Arabidopsis cDNAs in their entire lengths