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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 the representation of what you're looking for. Identifying enriched sites is a related but different task.
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
EMBOSS output format can be changed with the option, -rformat. See EMBOSS Report Formats for more details.
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 the command-line program and data files
# Search using all Transfac profiles match matrix.dat MyPromoters.fa MyPromoters.match_out.txt minSUM_good.prf # Search using a subset of profiles match matrix.dat MyPromoters.fa MyPromoters.vert.match_out.txt vertebrate_non_redundant_minSUM.prf
- Publication: 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
hmmsearch Pfam-A.hmm MyProteins.fa > MyProteins.Pfam-A.hmm.out.txt
Bioconductor packages