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