meme - Multiple Em for Motif Elicitation meme "$input1" -o "${html_outfile.files_path}" -nostatus ##-p 8 ##number of processors #if str( $options_type.options_type_selector ) == 'advanced': -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }" -${options_type.alphabet_type.alphabet_type_selector} -mod "${options_type.mod_type.mod_type_selector}" -nmotifs "${options_type.nmotifs}" -wnsites "${options_type.wnsites}" #if $options_type.evt < float('inf'): -evt "${options_type.evt}" #end if #if str( $options_type.mod_type.mod_type_selector ) != 'oops': #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites': -nsites "${options_type.mod_type.motif_occurrence_type.nsites}" #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites': -minsites "${options_type.mod_type.motif_occurrence_type.minsites}" -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}" #end if #end if #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact': -w "${options_type.motif_width_type.width}" #else -minw "${options_type.motif_width_type.minw}" -maxw "${options_type.motif_width_type.maxw}" #end if #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim': -nomatrim #else -wg "${options_type.motif_trim_type.wg}" -ws "${options_type.motif_trim_type.ws}" ${options_type.motif_trim_type.noendgaps} #end if #if str( $options_type.bfile ) != 'None': -bfile "${options_type.bfile}" #end if #if str( $options_type.pspfile ) != 'None': -psp "${options_type.pspfile}" #end if #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna": ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal} #end if -maxiter "${options_type.maxiter}" -distance "${options_type.distance}" -prior "${options_type.alphabet_type.prior_type.prior_type_selector}" #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone': -b "${options_type.alphabet_type.prior_type.prior_b}" #if str( $options_type.alphabet_type.prior_type.plib ) != 'None': -plib "${options_type.alphabet_type.prior_type.plib}" #end if #end if #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons': -cons "${options_type.alphabet_type.spmap_type.cons}" #else -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}" -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}" #end if #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch': -x_branch -bfactor "${options_type.branching_type.bfactor}" -heapsize "${options_type.branching_type.heapsize}" #end if ##-maxsize "1000000" ##remove hardcoded maxsize? should increase number of processors instead #end if 2>&1 || echo "Error running MEME." && mv ${html_outfile.files_path}/meme.html ${html_outfile} && mv ${html_outfile.files_path}/meme.txt ${txt_outfile} && mv ${html_outfile.files_path}/meme.xml ${xml_outfile} Basic Advanced Protein DNA simple Dirichlet prior mixture of Dirichlets prior extremely low variance dmix mega for all but last iteration of EM; dmix on last iteration add +1 to each observed count uni pam Use starting point from string simple Dirichlet prior mixture of Dirichlets prior extremely low variance dmix mega for all but last iteration of EM; dmix on last iteration add +1 to each observed count uni pam Use starting point from string One Occurrence Per Sequence Zero or One Occurrence Per Sequence Any Number of Repetitions Use defaults nsites min and max sites Use defaults nsites min and max sites Exact width Specify a range No motif trim Trim motif Perform x-branching No x-branching value == True

.. class:: warningmark **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.** If you want to specify sequence weights, you must include them at the top of your input FASTA file. .. class:: infomark **To cite MEME:** Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. For detailed information on MEME, click here_. To view the license_. ------ **Citation** If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* .. _here: http://meme.nbcr.net/meme/meme-intro.html .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html