Table 4

Test scenario 3 and 4: Difficult cases for reconstruction of gene structures

Tool

Ned kinesin

Phs dynactin p62

Hs dynactin p50

Pug coronin

Mm dynactin p150

Hs myosin

Th CAPα

Scipio 1.5¹

✓

✓

✓

✓

✓

✓

✓

Prosplign²

o

o

✓

-

✓

-

✓

Exonerate³

o

o

-

-

✓

-

-

Prot_map⁴

o

o

-

-

-

o

-

Fgenesh+⁵

o

o

-

-

-

o

o

Wise2⁶

o

o

-

-

-

-

-

Augustus⁷

o

o

-

-

-

-

-

Fgenesh⁵

o

o

-

-

-

-

-

Genscan⁸

o

o

-

-

-

-

-

BLAT⁹

o

o

-

-

-

-

-

Scipio 1.0¹

o

o

-

-

-

-

-

Ned: Neurospora discreta, Phs: Phytophthora sojae, Hs: Homo sapiens, Pug: Puccinia graminis, Mm: Mus musculus, Th: Thielavia heterothallica

✓ All exons are reconstructed correctly

o All annotated exons are matched by or overlap with predicted exons

- Exons are missing

¹ Ned, Phs: cross species default options; Hs, Mm: default options, exhaust_align_size = 15000; Pug, Th: default options (for detailed parameters see Figures 3, 4, and 5 and Additional file 5)

² Parameters: -full -two_stages

³ Parameters: --model protein2genome

⁴ Similarity: Weak; Search for one best alignment only (for more parameters see Additional file 5)

⁵ Organisms: Ned, Th: Neurospora crassa; Phs: Phytophtora; Hs: Human; Pug: Puccina; Mm: Mouse

⁶ Parameters: -both

⁷ Parameters: --genemodel = exactlyone; Organisms: Ned: --species = neurospora; Phs, Pug, Th: --species = generic; Hs, Mm: --species = human (for more parameters see Additional file 5)

⁸ Organism: Vertebrate; Suboptimal exon cutoff: 1.00

⁹ Parameters: -minScore = 15; Ned, Phs: -tileSize = 5 -minIdentity = 54 -oneOff = 1; Hs, Pug, Mm, Th: -tileSize = 7 -minIdentity = 81

Hatje et al. BMC Research Notes 2011 4:265   doi:10.1186/1756-0500-4-265