Changes between Version 11 and Version 12 of SOPs/enriched_tf_binding_sites
- Timestamp:
- 11/04/20 17:10:34 (4 years ago)
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SOPs/enriched_tf_binding_sites
v11 v12 8 8 9 9 ==== MEME ==== 10 Based on expectation maximization (deterministic optimization). Spurious motifs can be reduced by filtering the input sequences, for example based on fold enrichment and/or reducing the sequence length (eg. ~200bp regions within the summit) from MACS for TFs in ChIP-Seq data.10 The [[http://meme-suite.org/tools/meme|MEME]] function of the [[http://meme-suite.org/index.html|MEME Suite]] uses expectation maximization (deterministic optimization) to perform de novo motif discovery from sequence input. Spurious motifs can be reduced by filtering the input sequences, for example based on fold enrichment and/or reducing the sequence length (eg. ~200bp regions within the summit) from MACS for TFs in ChIP-Seq data. 11 11 12 12 Sample commands: … … 30 30 }}} 31 31 32 Tomtom can then be run to compare MEME motifs to database(s) of known motifs. It's part of the MEME suite.32 [[http://meme-suite.org/tools/tomtom|Tomtom]] can then be run to compare MEME motifs to database(s) of known motifs. It is part of the MEME suite. 33 33 34 34 {{{ … … 52 52 53 53 54 === De novo search for all DNA motifs that could represent Transcription Factor Binding Sites (TFBS) ===54 === Search for all DNA motifs that could represent Transcription Factor Binding Sites (TFBS) === 55 55 56 56 Source of the Motifs: 57 * Databases such as TRANSFAC or JASPAR57 * Databases such as TRANSFAC or [[http://jaspar.genereg.net|JASPAR]] 58 58 * Protein binding arrays (PBM). 59 59 * TFBS prediction programs. … … 76 76 * Public web site (older data): http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi 77 77 78 For position weight matrices (PWM) or regular expressions we can use programs like MAST. Most prediction programs have a setting to scan for TFBS for a given motif. Example of a MAST command (where "MEME_motifs.txt" is a MEME-format file of TFBS motifs).78 For position weight matrices (PWM) or regular expressions we can use programs like [[http://meme-suite.org/tools/mast|MAST]] or [[http://meme-suite.org/doc/fimo.html|FIMO]]. Most prediction programs have a setting to scan for TFBS for a given motif. Example of a MAST command (where "MEME_motifs.txt" is a MEME-format file of TFBS motifs). 79 79 80 80 {{{ … … 82 82 }}} 83 83 84 84 FIMO can be run using its web [[http://meme-suite.org/doc/fimo.html|interface]] or from the [[http://meme-suite.org/doc/fimo.html?man_type=web|command line]] using a single motif in MEME format on a set of sequences like this: 85 86 {{{ 87 fimo myMotif.meme mySequences.fa 88 }}} 89 90 When running from the command line, FIMO will create a directory called fimo_out where it places its output.
