= Searching for patterns or motifs in a DNA or protein sequence =

This 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.

== Search for a pattern (text, with optional choices at some positions) ==

[http://emboss.sourceforge.net/apps/cvs/emboss/apps/dreg.html dreg] (EMBOSS suite) - for nucleic acids
{{{
dreg -pattern "GGCC[ACGT]" -sequence My_promoters.fa -outfile My_promoters.GGCCN.dreg_out.txt
}}}

[http://emboss.sourceforge.net/apps/cvs/emboss/apps/preg.html preg] (EMBOSS suite) - for proteins
{{{
dreg -pattern "LPE[ACS]G" -sequence My_proteins.fa -outfile My_proteins.fa.LPEMG.preg_out.txt
}}}