MEME（预测motif）下载

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https://meme-suite.org/meme/meme-software/5.5.5/meme-5.5.5.tar.gzwget https://meme-suite.org/meme/meme-software/5.5.5/meme-5.5.5.tar.gz

tar zxf meme-5.5.5.tar.gz 

cd meme-5.5.5

pwd#查看现在地址，假设为$pwd,一定要是绝对路径

./configure --prefix=$pwd/meme/meme_install --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt

make

make test

make install

vim ~/.bashrc

export PATH=$pwd/meme/meme_install/bin:$PATH   

meme --help#查看安装是否成功

参数

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

使用

meme test.fa -dna -mod zoops -nmotifs 5 -minw 6 -maxw 50

#输入为test.fa

#选择dna

#模式为zoops

#nmotifs 想要生成的motif数量