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Hi Joo Sang, The cosmo package contains a function, rseq(), that allows you to generate random DNA sequences according to a kth order Markov model. The 0th order Markov model would simply generate each nucleotide according to frequencies you supply, regardless of what nucleotides were observed in previous positions. A kth order Markov model allows the probability of observing a given nucleotide to depend on the previous k positions. The function is designed to insert occurrences of a motif into these sequences, either according to the zero-or-one-occurrense-per-sequence (ZOOPS) model or the two-component-mixture (TCM) model that allows any number of motif occurrences per sequence. These motifs are specified through their position weight matrix. If you wanted to simulate sequences without any motif occurrences, you could set the rate parameter of the ZOOPS model to 0, for example. The main function of the package, cosmo(), searches DNA sequences for a shared motif; the output contains among other things an estimate of the transition matrix for the background model so you could use this function to estimate the transition matrix you would then feed to rseq(). The package was just submitted to Bioconductor and is included in Bioconductor 2.0. The version posted there is intended for R 2.5. If you're a Linux/Unix user, you can still install it with >install.packages("cosmo", rep="http://bioconductor.org/packages/2.0/bioc/") You might have to install the tkWidgets package first if you don't have it: >source("http://bioconductor.org/biocLite.R") >biocLite("tkWidgets") If you need a Windows binary, you can go to http://cosmoweb.berkley.edu/software.html The version posted there (1.0.1) is also slightly newer than the Bioconductor version 1.0.0. I will update the Bionconductor package soon. Oliver On 11/16/06, Joo Sang Lee <joosang at="" northwestern.edu=""> wrote: > Good evening. > > This question is maybe off-topic. I am sorry for this spam for most of you. > > I am studying the periodicity of DNA sequence. The approach I take is to > investigate the frequency of specific motif and distance between two > succesive occurrence of the motif. To acquire the frequency relative to > random sequence, I need to generate a random sequence with the same > composition of bases as original sequence. I am looking for the public > software to help me in calculating the relative frequency of getting random > sequences. I look forward to any of comments or advice on this problem. > Thank you very much. > > Best regards, > > Joo Sang Lee > Department of Physics, > Northwestern University > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi! > I need to generate a random sequence with the same > composition of bases as original sequence. I am looking for > the public software to help me in calculating the relative > frequency of getting random sequences. I look forward to > any of comments or advice on this problem. It seems you are looking for a virtual genome! http://www.virtualgenome.com Finally there is a practical appliance for this. :-))) Regards, Michael. -- ----------------------------------------------------------- Dipl.-Inform. Michael Nuhn Bioinformatik Zentrum f?r Nanostrukturtechnologie und Molekularbiologische Technologie +49 (0)631 - 205 4334 nuhn at rhrk.uni-kl.de http://nbc3.biologie.uni-kl.de/