• TSS/Promotor finders: TSSG and TSSW, Dragon Promoter Finder 1.2 ,NNPP2.1 , Promoter2.0, proscan, FunSiteP 2.1, PromoterInspector,HCtata
  TF: Dnanalyze, MatInspector, TFSEARCH, TESS, Signal Scan, TRANSFAC, rvista
  

principle genome resources:
wustl, BROAD, baylor, Sanger sequencing

• hapmap- human populations
• predone alignment: blastz vista
  • alignment: pipmaker AVID Dialign+Chaos zpicture alfresco synplot jdotter GLASS
  • visualisation pipmaker zpicture-linked to rVISTA
  • rVISTA (either analyzing BLASTZ output: zpicture, or the AVID alignment) VISTA Genome Browser
  • Divergence time: Human-Mouse (80Mio years), Anopheles/Drosophila (250 My), Mouse-Chicken (300Mio), Mouse-Frog (350Mio), Mouse-ZebraorFugu (450Mio), animal/fungi (1000My)
    mouse-human comparison is optimal for the identification of large (80-1000bp) functional gene-regulatory elements

• miRBase sequences
• miRBase targets
• microrna.org targets
• Rfam
• russel mirnas
• Deqor: sirna design
• E-rnai: rnai design
• Sfold siRNA design

• Genomes JGI euk microb Fugu Ciona Flybase Wormbase Arabidopsis Yeast GOLDBrugia

• Primaclad takes aligned sequences and predicts common primer, up to 5 positions can degenerate
• Prifi