Changes between Version 15 and Version 16 of SOP/PatternsMotifs


Ignore:
Timestamp:
08/25/17 10:15:22 (7 years ago)
Author:
krichard
Comment:

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  • SOP/PatternsMotifs

    v15 v16  
    5151
    5252[http://meme-suite.org/doc/meme-format.html/ MEME Suite] For protein binding motifs
    53  * Build a PWM from a series of aligned sequences using the "meme" command
     53 * Build a PWM from a series of aligned sequences using the [http://meme-suite.org/tools/mem/ meme] command
    5454{{{
    55 meme aligned_sequences.txt -protein -nmotifs 1 -w [width of motif] -o location_for_output_matrix
     55meme aligned_sequences.txt -protein -nmotifs 1 -w [width of motif] -o output_direftory
    5656}}}
    5757
    … …  
    6161    -w:           defines a width of a motif to find [optional].//
    6262
    63 Using the MAST program within the MEME-suite, with the PWM output by the above command you can search a list of protein sequences, in FASTA format, for your motif.
     63*  Using the [http://meme-suite.org/doc/mast.html/ MAST] program within the MEME-suite, with the PWM output by the above command you can search a list of protein sequences, in FASTA format, for your motif.
    6464{{{
    6565mast -minseqs 100 -m 1 -comp -ev 10 -o output_directory