Matrix Meme.html

matrix meme.html meme pron meem a contagious idea that replicates like a virus passed on from mind to mindmemes function the same way genes and viruses do propagating through communication networks and facetoface contact between people the root of the word memetics a field of study which postulates that the meme is the basic unit of cultural evolution, meme writes its output to files in a directory named memeout which it creates if necessary you can change the output directory using the o or oc options the directory will contain memehtml an html file that provides the results in an interactive humanreadable format, output writes meme motif format to standard output a probability matrix and optionally a logodds matrix are output for each motif in the file the probability matrix is computed using pseudocounts consisting of the background frequency see bg below multiplied by the total pseudocounts see pseudo below, a positionspecific scoring matrix pssm for use by the mast sequence database search program the position specific probability matrix pspm describing the motif created by memes internal em algorithm the first line of each motif section is called the motif summary line

meme can either a favor motifs that appear exactly once in each sequence in the training set the oneper model b favor motifs that appear zero or one time in each sequences in the training set the zerooroneper model or c give no preference to the number of occurrences the zeroormoreper model, meme is a tool for discovering motifs in a group of related dna or protein sequences a motif is a sequence pattern that occurs repeatedly in a group of related protein or dna sequences meme represents motifs as positiondependent letterprobability matrices which describe the probability of each possible letter at each position in the pattern

simplified positionspecific probability matrix meme motifs are represented by positionspecific probability matrices that specify the probability of each possible letter appearing at each possible position in an occurrence of the motif in order to make it easier to see which letters are most likely in each of the columns of the motif the , meme outputs its results primarily as an html file named memehtml meme also outputs a machinereadable xml file and a plaintext versions of its results named memexml and memetxt respectively these files are placed in a directory named memeout you can select for the directory to have a different name using the o or oc options, related questions in a poll 37 of the people polled answered yes to the question are you in favor of the death penalt two forces are acting at an angle 120 the bigger force is 40n and the resultant is perpendicular to, algorithm meme can either a favor motifs that appear exactly once in each sequence in the training set the oneper model b favor motifs that appear zero or one time in each sequences in the training set the zerooroneper model or c give no preference to the number of occurrences the zeroormoreper model