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I want to find conserved motig or seq patterns between regulatory sequence of 4 operons of bacteria. is there any tool for this purpose ? |
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Hello Shahid I tried MEME, http://meme.ebi.edu.au/meme/cgi-bin/meme.cgi, some time ago and i think it did a good job. I saw someone recommend Weeder also, http://159.149.109.9/modtools/ If you would rather have it as a program, i have heard about GimmeMotifs, http://131.174.221.43/bioinfo/gimmemotifs/index.htm but i have not tried it myself. Mvh Martin |
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Hi! Have you tried this tool, called "FootPrinter"? http://wingless.cs.washington.edu/htbin-post/unrestricted/FootPrinterWeb/FootPrinterInput2.pl 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 |
