= Searching for patterns, motifs, or profiles 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 profile (a probability matrix, with choices at all positions) ==

These searches are generally a two-step process, one step to create the motif and one step to search with it.  There are several choices of detailed options, so check out the documentation.

[http://emboss.sourceforge.net/apps/cvs/emboss/apps/prophecy.html prophecy] + [http://emboss.sourceforge.net/apps/cvs/emboss/apps/profit.html profit] (EMBOSS suite) - for proteins
{{{
prophecy -sequence Aligned_protein_sites.fa -type F -name MyProfile -outfile MyProfile.txt -filter
profit -infile MyProfile.txt -sequence My_proteins.fa -outfile My_proteins.MyProfileprofit_out.txt
}}}

[http://hmmer.org/ HMMER] - for proteins or nucleic acids
{{{
# Create a HMM from an aligned set of proteins or nucleic acids (fasta or other common format)
hmmbuild MyProfile.hmm Aligned_protein_sites.fa
# Use the HMM to search a fasta file of proteins
hmmsearch MyProfile.hmm Protein_set.fa > Protein_set.MyProfile.hmmsearch_out.txt
}}}