I would like to make the promoter comparison of one gene between Japonica and Indica cultivar.
Hi Tuyen,
If you mean a Promoter Predictor, there are several web-absed tools to analyze a specific genome region to find a probable region acting as promoter. To get better results you must try at least three different methods to get a consensus prediction. Some of those tool I recommend you are:
- NN based: http://www.fruitfly.org/seq_tools/promoter.html
- NN based: http://www.cbs.dtu.dk/services/Promoter/
- NN based: http://promotor.biosino.org/
- Suite of genomic tools: http://www.genetools.us/genomics/Promoter%20databases%20and%20prediction%20tools.htm
Good Luck!
Actually, you can use almost any bioinformatics tool, which is applicable for DNA sequence analysis. Just put there DNAs of your interest, set parameters of analysis and Go :) But before, read manuals/help to use the chosen tool for your particular purpose.
You can find a lot of useful info and tools at NCBI. See there, for example:
http://www.ncbi.nlm.nih.gov/guide/sequence-analysis/
And browse through the left side-bar menu at NCBI (http://www.ncbi.nlm.nih.gov/) to find more.
I am not sure if these genes have functional divergence. anyways i think you should look of defined promoter elements in the nucleotide sequence upstream to ATG. usually 1 Kb sequence is good enough but it is worth to compare about 3 Kb upstream region in both the genes. As other Researchers mentioned above there are several tools like PLACE or PlantCARE etc. All the best
I think PLACE Web is very good program Signal Scan
http://www.dna.affrc.go.jp/PLACE/signalscan.html
I hope this may help
Be VERY careful!
All of these promoter prediction tools are just dry lab and give you predictions. They do NOT give you any promoter elements at all, merely sequences that have similarity to known elements. You can use the dry lab comparisons to guide your wet lab work on promoter analysis but you cannot get information on promoter function without actually doing the experiments.
PLACE and PlantCare are hopelessly out of date and you will get a lot of mainly meaningless predictions. For example, MYB binding sites are AT-rich and you will get lots of potential binding sites that are not functionally relevant.
The one advantage that you have is that you are comparing two orthologues from the two rice species and the similarities in promoter sequence (if the genes show the same expression characteristics) could be revealing.
I work on plants and would be happy to give any advice that you may need.
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