AlignAce - Aligns Nucleic Acids Conserved Elements AlignAce is a Gibbs Sampler written for Yeast Genes, the original package includes sophisticated tools to rank and cluster found motifs Roth, FR, Hughes, JD, Estep, PE, GM Church http://atlas.med.harvard.edu/ 99788350 http://arep.med.harvard.edu/pdf/Roth98.pdf source for Linux license.txt http://ftp.bioinformatics.org/pub/jannotatix/plugins/alignace.zip http://ftp.bioinformatics.org/pub/jannotatix/plugins/alignace.zip AlignACE AlignACE.exe (no Description available) (no Description available) 10 Width 10 Number of columns to align (REM: This is the length/width of the motif) 10 Expected Sites 10 Number of sites expected in model 0.38 GC Content 0.38 Background fractional GC content of input sequence (REM: The default value reflects the yeast genome, the value a. thaliana is 0.36) 200 Min. Passes 200 Minimum number of non-improved passes in phase 1 1 Oversample 1 possible sites / (expect * numcols * seedings) 1 Undersample 1 1/undersample ProfileID SiteSequence SequenceNumber Start Strand ProfileScore MotifSampler Motif Sampler is a Gibbs Motif Sampler from the PlantCare team Thijs G., Lescot M., Marchal K., Rombauts S., De Moor B., Rouze P., Moreau Y. http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html 11751219 http://bioinformatics.oupjournals.org/cgi/reprint/17/12/1113 web / binary for Linux and Windows http://ftp.bioinformatics.org/pub/jannotatix/plugins/motifsampler.zip http://ftp.bioinformatics.org/pub/jannotatix/plugins/motifsampler.zip MotifSampler MotifSampler.exe (no Description available) (no Description available) 8 Width 8 The exact width of the motif has to be known in advance! /home/max/JannotatixPlugins/MotifSampler/athaliana_3.bg Background Model athaliana_3.bg A hidden markov model that estimates the probability that a given sequence is produced by intergenic-sequence noise 1 Strand 1 Search both (1) or only one strand (0) 0 1 0.2 Prior 0.2 The a priori probability that a sequence contains a motif 0 Max. Instances 0 Maximum number of instances or 0 to deactivate limit 1 Number of Motifs 1 Number of motifs to search for 1 Iterations 1 Number of iterations, the algorithm is simply repeated this number of times Sequence Source Start End Score Strand ProfileID Multiple EM for Motif Elicitation Timothy Bailey, Charles Elkan, Bill Grundy http://meme.sdsc.edu 7584402 http://www.sdsc.edu/~tbailey/papers/ismb94.ps web / sourcecode for unix Meme/COPYRIGHT http://ftp.bioinformatics.org/pub/jannotatix/plugins/meme.zip http://ftp.bioinformatics.org/pub/jannotatix/plugins/meme.zip meme-linux/bin/meme (no Description available) STDOUT (no Description available) zoops Distribution of motifs zoops One Occurrence Per Sequence (oops), Zero or One Occurrence Per Sequence (zoops) or Two-Component Mixture (tcm) oops zoops tcm 1 Maximum number of motifs 1 The number of *different* motifs to search for 1 Number of sites 1 The (expected) number of occurrences of each motif. If -nsites is given, only that number of occurrences is tried. These switches are ignored if mod = oops. 8 Minimal Width 8 Minimal width of the motif to try 25 Maximal Width 25 Maximal width of the motif to try Background Model The name of the file containing the background model for sequences. 50 Max Iterations 50 The number of iterations of EM to run from any starting point. false Look on reverse strand false motifs occurrences may be on the given DNA strand or on its reverse complement. Default: look for DNA motifs only on the strand given in the training set. false Look for palindromes false Choosing -pal causes MEME to look for palindromes in DNA datasets. <p> MEME averages the letter frequencies in corresponding columns of the motif (PSPM) together. For instance, if the width of the motif is 10, columns 1 and 10, 2 and 9, 3 and 8, etc., are averaged together. The averaging combines the frequency of A in one column with T in the other, and the frequency of C in one column with G in the other. dirichlet Distribution of prior dirichlet The prior distribution on the model parameters: <p> dirichlet == simple Dirichlet prior This is the default for -dna and -alph. It is based on the non-redundant database letter frequencies.<p> dmix == mixture of Dirichlets prior. This is the default for -protein.<p> mega == extremely low variance dmix; variance is scaled inversely with the size of the dataset.<p> megap == mega for all but last iteration of EM; dmix on last iteration.<p> addone == add +1 to each observed count<p> dirichlet dmix mega megap addone skip strange matrix trimming steps Output as Text Assume DNA alphabet Print motifs in fasta format AlignmentID Ignore Ignore Sequence Start Score SiteSequence PlantCare Plantcare is a database of plant cis-acting regulatory elements, many of them from Arabidopsis Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P, Rombauts S. http://oberon.fvms.ugent.be:8080/PlantCARE/index.html 11752327 http://www.ncbi.nlm.nih.gov/fullTEXT website http://ftp.bioinformatics.org/pub/jannotatix/plugins/plantcare.zip http://ftp.bioinformatics.org/pub/jannotatix/plugins/plantcare.zip PlantCare Main Server me Test http://oberon.fvms.ugent.be:8080/care-bin/CallMat_NN47.htpl (no Description available) Search This parameter has to be specified Sequence Strand Start Score