Changes between Initial Version and Version 1 of SOP/PatternsMotifs


Ignore:
Timestamp:
07/22/16 09:41:28 (8 years ago)
Author:
gbell
Comment:

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  • SOP/PatternsMotifs

    v1 v1  
     1= Searching for patterns or motifs in a DNA or protein sequence =
     2
     3This is a traditional bioinformatics task, any many tools do this in a variety of ways.  One main determinant of tool is your representation of what you're looking for.
     4
     5== Search for a pattern (text, with optional choices at some positions) ==
     6
     7[http://emboss.sourceforge.net/apps/cvs/emboss/apps/dreg.html dreg] (EMBOSS suite) - for nucleic acids
     8{{{
     9dreg -pattern "GGCC[ACGT]" -sequence My_promoters.fa -outfile My_promoters.GGCCN.dreg_out.txt
     10}}}
     11
     12[http://emboss.sourceforge.net/apps/cvs/emboss/apps/preg.html preg] (EMBOSS suite) - for proteins
     13{{{
     14dreg -pattern "LPE[ACS]G" -sequence My_proteins.fa -outfile My_proteins.fa.LPEMG.preg_out.txt
     15}}}
     16