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Given a sequence, how to automatically figure out where are promoters, enhancers - (Oct/24/2006 )

Given a DNA sequence, what is the way to figure out where is promoter, enhancer, AmpR, KanR, T7 Tag ...?

Here is the best way I found:

1. Go to If you don't have an account, login with user name "guest" and password "BxAF".
2. Paste sequence directly into the big textarea box and click "Update Edited File" link! This is critical! The program automatically conversion non-formatted sequence to GenBank format.
3. Click link "Auto-Annotation" and click link "View Predicted Features". You can directly click button "Add Predicted Features" to add features to the GenBank file.

That is it! Here is a test with pCDNA3 sequence:

Feature Location Label
promoter 863..879 T7 Promoter
primer_bind complement(3271..3294) M13/pUC universal reverse primer
primer_bind 863..882 T7 universal primer (Invitrogen)
primer_bind 863..881 T7 universal primer (pET vectors)
primer_bind complement(1022..1039) BGH reverse primer
primer_bind complement(3270..3285) M13/pUC Reverse Sequencing Primer (-24)
primer_bind complement(3290..3309) M13/pUC Reverse Sequencing Primer (-48)
primer_bind complement(3270..3288) M13 pBluescript Reverse Sequencing Primer
enhancer 1753..1824 SV40 early promoter enhancer
enhancer 1825..1896 SV40 early promoter enhancer
enhancer 309..715 CMV immediately early promoter enhancer
promoter 863..882 T7 promoter
misc_feature 4433..5292 Ampicillin


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