I want to find conserved motig or seq patterns between regulatory sequence of 4 operons of bacteria. is there any tool for this purpose ?
asked 19 Oct '12, 13:05
If you would rather have it as a program, i have heard about GimmeMotifs, http://18.104.22.168/bioinfo/gimmemotifs/index.htm but i have not tried it myself.
answered 19 Oct '12, 14:20
Have you tried this tool, called "FootPrinter"?
It appears to look for motifs in a set of homologous input sequences. The user needs to supply the sequences and also a phylogenetic tree in which your bacterials are included. (There is a "default tree" including some bacterias). I have not tried it myself (I have not worked with bacterias) but if I have understood your problem correctly it might be usable...
Best wishes, Malin Larsson
answered 19 Oct '12, 14:34