Searching for patterns, motifs, or profiles in a DNA or protein sequence

This is a traditional bioinformatics task, and many tools do this in a variety of ways. One main determinant of tool is your representation of what you're looking for.

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

​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

​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

​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

​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 with a custom 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.

​prophecy + ​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

​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

​JASPAR - for transcription factor binding sites

Search with a dataset of profiles

​JASPAR - for transcription factor binding sites

• Select a JASPAR CORE database (like ​Vertebrata) to search your DNA sequence(s) with the set of profiles

​TRANSFAC's match - for transcription factor binding sites

• commercial application requiring a license for the most up-to-date version
• Whitehead only: See BaRC_datasets/Transfac for command-line program
• Publication: [​http://www.ncbi.nlm.nih.gov/pubmed/12824369 Kel et al., 2003
• Public web site (older data): ​http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi

​HMMER - for proteins or nucleic acids

• Use a set of HMMs (like Pfam or another public protein domain resource) to search a fasta file of proteins