Changes between Version 19 and Version 20 of SOP/PatternsMotifs

Timestamp:

10/24/19 10:52:34 (5 years ago)

Author:

gbell

Comment:

--

SOP/PatternsMotifs

@@ -40 +40 @@
 [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)
+# Create a HMM from a 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
@@ -48 +48 @@
 [http://jaspar.genereg.net/ JASPAR] - for transcription factor binding sites
 
-[http://meme-suite.org/doc/meme-format.html/ MEME Suite] For proteins
- * Build a PWM from a series of aligned sequences using the [http://meme-suite.org/tools/mem/ meme] command
+[http://meme-suite.org/ MEME Suite] For proteins or nucleic acids 
+ * Build a PWM from a series of sequences using the [http://meme-suite.org/tools/meme meme] command
 {{{
-meme aligned_sequences.fa -protein -nmotifs 1 -w [width of motif] -o output_directory
+meme Sequence_set.fa -protein -nmotifs 5 -minw 8 -maxw 12 -o output_directory
 }}}
 
 Program options:
     -protein:   specifies your input sequences are amino acids.\\
+    -dna:   specifies your input sequences are DNA nucleotides.\\
     -nmotifs:  indicates the number of motifs to look for in your sequences\\
-    -w:           defines a width of a motif to find [optional].//
+    -minw, -maxw:           minimum and maximum motif widths//
 
 *  Using the [http://meme-suite.org/doc/mast.html/ MAST] program within the MEME-suite, with the PWM output by the above command you can search a list of protein sequences, in FASTA format, for your motif.