I am not related with this area, but I would like to make some predictions about promoters of two particulars genes.
Software's for promoter analysis:
1. JasPar (jaspar.cgb.ki.se/)
2. Toucan (http://homes.esat.kuleuven.be/~saerts/software/toucan.php)
3. MAPPER2 (http://genome.ufl.edu/mapper/run/?init=db)
4. Perl module (http://tfbs.genereg.net/)
5. UCSC (http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=295670123&clade=mammal&org=Human&db=hg19&hgta_group=regulation&hgta_track=tfbsConsSites&hgta_table=0&hgta_regionType=genome&position=chr21%3A33031597-33041570&hgta_outputType=primaryTable&hgta_outFileName=)
6. ChIP and Microarray (http://jjwanglab.org/ChIP-Array)
7. ConTraV2 (http://bioit.dmbr.ugent.be/contrav2/index.php)
Hope this helps!
This question is too unspecific.
If you are working in procaryotes, I would say: try PRODORIC http://www.prodoric.de/
Otherwise let me know what you need and I may be able to help.
Hello Santiago,
A huge variety of software are available working on different algorithm to analyze the promoters. Basically, most of the programme search for the 6-10bp cis-elements present in the DNA sequences. I find PLACE as a best programme to find these cis elements. Afterwards, manually analyzing the position of cis-elements and density distribution among the whole length may give you some predictions about the promoter modular structure.
Check it
If you are interested in TF binding sites, MatInspector by Genomatix is top notch. If your institute can afford a proprietary software, that is. They do (hopefully still) offer free trials, which should be good enough if you are to do one-time single promoter analysis.
Pedro, you are right. I am interested in a eukaryotic promoter, particularly of plants. I will prove all the programs you recommend. Thank you at all!
Software's for promoter analysis:
1. JasPar (jaspar.cgb.ki.se/)
2. Toucan (http://homes.esat.kuleuven.be/~saerts/software/toucan.php)
3. MAPPER2 (http://genome.ufl.edu/mapper/run/?init=db)
4. Perl module (http://tfbs.genereg.net/)
5. UCSC (http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=295670123&clade=mammal&org=Human&db=hg19&hgta_group=regulation&hgta_track=tfbsConsSites&hgta_table=0&hgta_regionType=genome&position=chr21%3A33031597-33041570&hgta_outputType=primaryTable&hgta_outFileName=)
6. ChIP and Microarray (http://jjwanglab.org/ChIP-Array)
7. ConTraV2 (http://bioit.dmbr.ugent.be/contrav2/index.php)
Hope this helps!
If you go to www.arabidopsis.org there is a link for TSSP-TCM plant promoter identification. I have not used this software as I work with prokaryotes. But the reference for this can be found in Nucleic acid research Shahmuradov et al. 2005. Hope it is useful.
Hola Santiago, if instead of searching elements in just one promoter you need to compare your promoter to others or to a reference sequence, I would suggest MEME Suite (free & online). MEME allows you to first find common conserved motifs and then you can see with the same application if these have being previously described as essential transcriptional boxes. Its like a reverse kind of search. It works for protein domains as well. What i like is that you can visualize a consensus sequence based on the sequences you analyse. PLACE is good but it will find too many false positive elements. Good luck!
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