Table 1.
Programs and parameters used for evaluation
| Name | Version | Options |
|---|---|---|
| Blat | 34 | –noHead -q=rna -fine -noTrimA |
| BlatX | 34 | –noHead -q=rna -noTrimA |
| est2genome | 5.0.0-2 | –stdout -auto -align |
| est2genome+ | 5.0.0-2 | –stdout -auto -align |
| –mismatch 3 -intronpenalty 20 | ||
| –splicepenalty 10 -minscore 10 | ||
| Exalin | 2005-05-06 | –p HumanSPM.par -a 1 |
| Exonerate | 2.0.0 | –model est2genome |
| –showalignment no -n 1 | ||
| ExonerateDG | 2.0.0 | –model cdna2genome |
| –showalignment no -n 1 | ||
| ExonerateCG | 2.0.0 | –model coding2genome |
| –showalignment no -n 1 | ||
| GeneSeqer | 4.0 | [species] |
| GMap | 2007-09-28 | –format=3 |
| Pairagon | 1.1 | |
| PairagonX | 1.1 | –cross |
| Palma | 0.3.7 | –bestAlignmentOnly |
| sim4 | 2003-09-21 | A=4 |
| sim4+ | 2003-09-21 | A=4 N=1 |
| Spaln | 070830 | –O1 |
| SpalnX | 070830 | –O1 -yX |
| Spidey | 1.40 | |
| SpideyX | 1.40 | –sT |
| Splign | 1.31 | |
| SplignX | 1.31 | –disc |
| Xat | 0.8.6 | outflag=0 |