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: |
| ESTs | -B0 -V10000 -E1e-10 | |
| cDNA sequence reads | Sim4 | |
| BDGP cDNAs | -A 4 | |
| GenBank cDNAs | ||
| ARGS | ||
| Sim4 [18] | Non-coding RNAs | -A 4 |
| WU-BLASTX [20] | Fly | -B800 -V800 -Z300000 -E1e-10 |
| Community reports | ||
| WU-BLASTX | Non-fly | -B800 -V800 -Z300000 -E1e-10 |
| SEG+XNU | ||
| WU-TBLASTX | dbEST (insect) | -B200 -V200 -Z300000 -E1e-10 |
| UniGene (rodent) | SEG+XNU | |
| Genie [42] | ||
| Genscan [43] | ||
| tRNAscan-SE [44] | ||
| McPromoter [45] | ||
| ClustalW [34] | version 1.8 | |
| Align | ||
| InterProScan [32] |