|
Software used in the analysis pipeline |
||
| 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] |
||
Mungall et al. Genome Biology 2002 3:research0081.1 doi:10.1186/gb-2002-3-12-research0081 |
||