Table 1 Software used in the analysis pipeline
From: An integrated computational pipeline and database to support whole-genome sequence annotation
Program | Data source | Parameters |
|---|---|---|
RepeatMasker [41] | Transposable elements | -parallel 2 -nolow -keepmasked |
Sim4wrap | Gadfly Release2 | BLAST: |
| Â | ESTs | -B0 -V10000 -E1e-10 |
| Â | cDNA sequence reads | Sim4 |
| Â | BDGP cDNAs | -A 4 |
| Â | GenBank cDNAs | Â |
| Â | ARGS | Â |
Sim4 [18] | Non-coding RNAs | -A 4 |
WU-BLASTX [20] | Fly | -B800 -V800 -Z300000 -E1e-10 |
| Â | Community reports | Â |
WU-BLASTX | Non-fly | -B800 -V800 -Z300000 -E1e-10 |
| Â | Â | SEG+XNU |
WU-TBLASTX | dbEST (insect) | -B200 -V200 -Z300000 -E1e-10 |
| Â | UniGene (rodent) | SEG+XNU |
Genie [42] | Â | Â |
Genscan [43] | Â | Â |
tRNAscan-SE [44] | Â | Â |
McPromoter [45] | Â | Â |
ClustalW [34] | Â | version 1.8 |
Align | Â | Â |
InterProScan [32] | Â | Â |