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How to predict a promoter region for a gene - Promoter cloning + genes into vector (Aug/20/2005 )

hi there,

Presently, i given a task to find the promoter region for a gene of interest and to clone this promoter+ gene into a vector.

The problem is that there ain't many program i found through internet search that enables bacterial promoter predictions. I found about two programs and enter in my DNA sequence and the results from both does not tally.

Furthermore, even with the results that predicts the -35 and -10 promoter box ..there questions like from where on the DNA sequence should i design a pair of primer that will include the promoter + gene of interest? It should include in the -35 and -10 regions right?

Can anyone please enlighten me...

Is there any program that u know of enable bacterial promoter prediction?

Any help will be appreciated.. thanks..


You can use the Gene2Promoter program available in the Genomatix suite of programs, however their coverage of bacterial genomes are limited.

The available genomes for this software are:
Anopheles gambiae
Arabidopsis thaliana
Canis familiaris
Drosophila melanogaster
Gallus gallus
Homo sapiens
Mus musculus
Oryza sativa
Pan troglodytes
Plasmodium falciparum
Rattus norvegicus

Hope this helps.


u can use a tchnique to predict the promoter region ...take the mRNA of the gene of interest and then blast with the whole genome of that particular organism.Click the blast hit having 100% match.Then either the genemap or the genbank flat file of that orgaism will open .In the gene map u can see a portion mentioned like this "100% blast" and that portion will be designated as that particular gene of interest ..u take some 2000 base pairs above that and 2000 base pairs below that .then do clustalW or Blast2 alignment that again with mRNA .the mRNA will show 100 % alignment just before is the promoter region and after that there is the structural gene part .so u can take some 200 or 300 or as u like as promoter region before the alignment of mRNA and from the alignment towards below as the structural part of gene of interest .
hope this will help u .


I believe that if you are dealing with bacterial promoter, sequences -300bp of start codon will do.


i want to know have plants totally different transcriptionb factors ..when i took the promoter region of a plant and put that in TF search for transcription factor binding sites ..i set the taxonomy as plants ..and i got only one transcription factor binding site for the plant ..i also anlyzed another plant and do the analysis in the same also obtained the same result ....when i took the promoter of the same gene of animals and set the taxonomy accordinf to the organism i got so many tfs of animals ...but the plant having the facor is not found in any animal ...was i right the chhosing the taxonomy or i should set the taxonomy as all ..
plz help me


yes, plant are quite different.

Which program did you use?


QUOTE (cyberpostdoc @ Sep 5 2005, 10:57 AM)
yes, plant are quite different.

Which program did you use?

i used the program TFsearch ......and in that i selected the the classification matrix according to the species like plants for plant .....vertebrate for man , mouse ...but i got only 2 tfs for plants ..and more for man and mouse ..was the right way to chose the classification matrix ..or i should select all....for the matrix
plz help me