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gene prediction tools - (Jan/29/2008 )

Hi, i would like to know which software/program from the internet to be used to predict active site in the gene?
And which program is 'trustworthy' for transcription factor prediction? As i know, there are a few programs such as AliBaba2, TRANSFAC etc....
It gives different results.
To analyze a gene which consists of promoter and ORF, i've tried softberry, augustus, gene builder, expasy etc....
Is there any other better software that is user friendly and not so complicated?
Please help....thank you.


i have used softberry and it works nicely, at least for plants. it has the option for an output pdf file to view your results graphically