Promoter Prediction Program
♦ 2.3k wrote:Just a very quick question on promoter prediction software. Has anyone used any of the available tools and if so do you have any recommendations on a) the fastest b) the most accurate, and c) the best of both?Here is a of some I found! Are any of these scalable to whole-genome data? Are there any others not included here?Of course if promoter prediction programs aren't the best way to retrieve these data (i.e. Promoter sequences +/- first exon), then I'm open to suggestions:) I'm looking to do this for Hymenoptera (i.e. Ant, bees, wasps).Cheers,Steve.
Plant Promoter Analysis
2.2k wrote:I've used an approach called phylogenetic printing years ago and I'm sure it has new updates now. Basically, this algorithm takes in homologous non-coding sequences (for example, 5'-flanking regions of the same gene from multiple species) and tries to find evolutionary conserved DNA elements (short stretches of nucleotides) based on sequence conservation and species phylogenetic tree. In theory, these elements are potential regulatory elements but you never know until you actually do the transgenic experiments.
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Promoter Scan
With this approach, I managed to find TATA-box in a lot of cases, so it seems to be working. ♦ 3.2k wrote:I have no experience with promoter discovery but an alternative approach would be to look for motifs directly upstream (and perhaps also downstream) of genes. I did a survey project on that for a Bioinformatics class.You would need to have the genes discovered and moreover you would need to select sets of genes that may be co-regulated.Weeder is one of the best motif discovery tools. Very fast and one of the beast in terms of accuracy (I can find the manuscript that did and exensive comparison of motif discovery tools and found Weeded to be the best). You have to give it a set sequences upstream of the genes that you think may have similar regulatory elements.From what I've read, all unsupervised motif discovery methods still have very disappointing sensitivity.On the Weeder there is also a suggestion of Pscan (2009):NEW If you are looking forover-represented motifs in promotersequences, perhaps you can also findour brand new tool, Pscan useful.