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b/softwares_config/meme_5.4.1.config |
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Usage: meme <dataset> [optional arguments] |
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<dataset> file containing sequences in FASTA format |
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[-h] print this message |
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[-o <output dir>] name of directory for output files |
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will not replace existing directory [-oc <output dir>] name of directory for output files |
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will replace existing directory [-text] output in text format (default is HTML) |
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[-objfun classic|de|se|cd|ce] objective function (default: classic) [-test mhg|mbn|mrs] statistical test type (default: mhg) |
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[-use_llr] use LLR in search for starts in Classic mode [-neg <negdataset>] file containing control sequences |
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[-shuf <kmer>] preserve frequencies of k-mers of size <kmer> when shuffling (default: 2) |
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[-hsfrac <hsfrac>] fraction of primary sequences in holdout set (default: 0.5) |
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[-cefrac <cefrac>] fraction sequence length for CE region (default: 0.25) |
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[-searchsize <ssize>] maximum portion of primary dataset to use for motif search (in characters) |
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[-maxsize <maxsize>] maximum dataset size in characters [-norand] do not randomize the order of the input |
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sequences with -searchsize [-csites <csites>] maximum number of sites for EM in Classic mode |
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[-seed <seed>] random seed for shuffling and sampling [-dna] sequences use DNA alphabet |
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[-rna] sequences use RNA alphabet [-protein] sequences use protein alphabet |
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[-alph <alph file>] sequences use custom alphabet [-revcomp] allow sites on + or - DNA strands |
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[-pal] force palindromes (requires -dna) [-mod oops|zoops|anr] distribution of motifs |
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[-nmotifs <nmotifs>] maximum number of motifs to find [-evt <ev>] stop if motif E-value greater than <evt> |
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[-time <t>] quit before <t> seconds have elapsed [-nsites <sites>] number of sites for each motif |
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[-minsites <minsites>] minimum number of sites for each motif [-maxsites <maxsites>] maximum number of sites for each motif |
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[-wnsites <wnsites>] weight on expected number of sites [-w <w>] motif width |
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[-minw <minw>] minimum motif width |
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[-maxw <maxw>] maximum motif width |
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[-allw] test starts of all widths from minw to maxw |
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[-nomatrim] do not adjust motif width using multiple |
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alignment |
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[-wg <wg>] gap opening cost for multiple alignments |
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[-ws <ws>] gap extension cost for multiple alignments |
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[-noendgaps] do not count end gaps in multiple alignments |
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[-bfile <bfile>] name of background Markov model file |
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[-markov_order <order>] (maximum) order of Markov model to use or create |
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[-psp <pspfile>] name of positional priors file |
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[-maxiter <maxiter>] maximum EM iterations to run |
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[-distance <distance>] EM convergence criterion |
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[-prior dirichlet|dmix|mega|megap|addone] |
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type of prior to use |
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[-b <b>] strength of the prior |
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[-plib <plib>] name of Dirichlet prior file |
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[-spfuzz <spfuzz>] fuzziness of sequence to theta mapping |
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[-spmap uni|pam] starting point seq to theta mapping type |
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[-cons <cons>] consensus sequence to start EM from |
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[-brief <n>] omit sites and sequence tables in |
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output if more than <n> primary sequences |
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[-nostatus] do not print progress reports to terminal |
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[-p <np>] use parallel version with <np> processors |
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[-sf <sf>] print <sf> as name of sequence file |
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[-V] verbose mode |
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[-version] display the version number and exit |