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

From: Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio

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 - - - - -
  1. Ned: Neurospora discreta, Phs: Phytophthora sojae, Hs: Homo sapiens, Pug: Puccinia graminis, Mm: Mus musculus, Th: Thielavia heterothallica
  2. All exons are reconstructed correctly
  3. o All annotated exons are matched by or overlap with predicted exons
  4. - Exons are missing
  5. 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)
  6. 2 Parameters: -full -two_stages
  7. 3 Parameters: --model protein2genome
  8. 4 Similarity: Weak; Search for one best alignment only (for more parameters see Additional file 5)
  9. 5 Organisms: Ned, Th: Neurospora crassa; Phs: Phytophtora; Hs: Human; Pug: Puccina; Mm: Mouse
  10. 6 Parameters: -both
  11. 7 Parameters: --genemodel = exactlyone; Organisms: Ned: --species = neurospora; Phs, Pug, Th: --species = generic; Hs, Mm: --species = human (for more parameters see Additional file 5)
  12. 8 Organism: Vertebrate; Suboptimal exon cutoff: 1.00
  13. 9 Parameters: -minScore = 15; Ned, Phs: -tileSize = 5 -minIdentity = 54 -oneOff = 1; Hs, Pug, Mm, Th: -tileSize = 7 -minIdentity = 81