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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]