Changes between Version 2 and Version 3 of SOP/PatternsMotifs

Timestamp:

07/22/16 10:36:06 (8 years ago)

Author:

gbell

Comment:

--

SOP/PatternsMotifs

@@ -1 @@
-= Searching for patterns or motifs in a DNA or protein sequence =
+= 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.
@@ -27 +27 @@
 
 
-== Search for a motif (a probability matrix, with optional choices at all positions) ==
+== 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 (fasta or other common format)
+hmmbuild Aligned_protein_sites.hmm Aligned_protein_sites.fa
+# Use the HMM to search a fasta file of proteins
+hmmsearch Aligned_protein_sites.hmm Protein_set.fa
+}}}