| | 50 | |
| | 51 | [http://jaspar.genereg.net/ JASPAR] - for transcription factor binding sites |
| | 52 | * Select a JASPAR CORE database (like [http://jaspar.genereg.net/cgi-bin/jaspar_db.pl?rm=browse&db=core&tax_group=vertebrates "Vertebrata"]) to search your DNA sequence(s) with the set of profiles |
| | 53 | |
| | 54 | [http://www.biobase-international.com/wp-content/uploads/2012/03/Match_command_line.txt TRANSFAC's match] - for transcription factor binding sites |
| | 55 | * commercial application requiring a license for the most up-to-date version |
| | 56 | * Whitehead only: See BaRC_datasets/Transfac for command-line program |
| | 57 | * Publication: [http://www.ncbi.nlm.nih.gov/pubmed/12824369 Kel et al., 2003 |
| | 58 | * Public web site (older data): http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi |
| | 59 | |
| | 60 | [http://hmmer.org/ HMMER] - for proteins or nucleic acids |
| | 61 | * Use a set of HMMs (like Pfam or another public protein domain resource) to search a fasta file of proteins |
