Changes between Version 1 and Version 2 of SOP/PatternsMotifs


Ignore:
Timestamp:
07/22/16 10:02:57 (9 years ago)
Author:
gbell
Comment:

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  • SOP/PatternsMotifs

    v1 v2  
    55== Search for a pattern (text, with optional choices at some positions) ==
    66
    7 [http://emboss.sourceforge.net/apps/cvs/emboss/apps/dreg.html dreg] (EMBOSS suite) - for nucleic acids
     7[http://emboss.sourceforge.net/apps/cvs/emboss/apps/dreg.html dreg] (EMBOSS suite) - for nucleic acids (where "pattern" is a regular expression)
    88{{{
    99dreg -pattern "GGCC[ACGT]" -sequence My_promoters.fa -outfile My_promoters.GGCCN.dreg_out.txt
    1010}}}
    1111
    12 [http://emboss.sourceforge.net/apps/cvs/emboss/apps/preg.html preg] (EMBOSS suite) - for proteins
     12[http://emboss.sourceforge.net/apps/cvs/emboss/apps/preg.html preg] (EMBOSS suite) - for proteins (where "pattern" is a regular expression)
    1313{{{
    1414dreg -pattern "LPE[ACS]G" -sequence My_proteins.fa -outfile My_proteins.fa.LPEMG.preg_out.txt
    1515}}}
    1616
     17[http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html fuzznuc] (EMBOSS suite) - for nucleic acids (where "pmismatch" is the number of mismatches in the pattern)
     18{{{
     19fuzznuc -pattern "nnnGGCCTnnn" -sequence My_promoters.fa -pmismatch 1 -outfile My_promoters.GGCCT.1mis.fuzznuc_out.txt
     20}}}
     21
     22[http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzzpro.html fuzzpro] (EMBOSS suite) - for proteins (where "pmismatch" is the number of mismatches in the pattern)
     23{{{
     24fuzzpro -pattern "xxxxLPEAGxxxx" -sequence My_proteins.fa -pmismatch 1 -outfile My_proteins.LPEAG.1mis.fuzzpro_out.txt
     25}}}
     26
     27
     28
     29== Search for a motif (a probability matrix, with optional choices at all positions) ==
     30