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)

​dreg (EMBOSS suite) - for nucleic acids

dreg -pattern "GGCC[ACGT]" -sequence My_promoters.fa -outfile My_promoters.GGCCN.dreg_out.txt

​preg (EMBOSS suite) - for proteins

dreg -pattern "LPE[ACS]G" -sequence My_proteins.fa -outfile My_proteins.fa.LPEMG.preg_out.txt