= 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 (where "pattern" is a regular expression)
{{{
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 (where "pattern" is a regular expression)
{{{
dreg -pattern "LPE[ACS]G" -sequence My_proteins.fa -outfile My_proteins.fa.LPEMG.preg_out.txt
}}}

[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)
{{{
fuzznuc -pattern "nnnGGCCTnnn" -sequence My_promoters.fa -pmismatch 1 -outfile My_promoters.GGCCT.1mis.fuzznuc_out.txt
}}}

[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)
{{{
fuzzpro -pattern "xxxxLPEAGxxxx" -sequence My_proteins.fa -pmismatch 1 -outfile My_proteins.LPEAG.1mis.fuzzpro_out.txt
}}}



== Search for a motif (a probability matrix, with optional choices at all positions) ==