Changes between Version 7 and Version 8 of SOP/PatternsMotifs

Timestamp:

07/28/16 10:38:20 (9 years ago)

Author:

gbell

Comment:

--

SOP/PatternsMotifs

@@ -55 +55 @@
   * 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
+{{{
+# 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: [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
 
 [http://hmmer.org/ 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
+}}}
+
+[http://www.bioconductor.org/ Bioconductor] packages
+  * [http://bioconductor.org/packages/release/bioc/html/TFBSTools.html TFBSTools]