* searchp: example search file for the search program * version = 1.01 of searchp 2004 Aug 25 * * documentation on the search program: * https://alum.mit.edu/www/toms/delila/search.html * This is an example search parmeter file for the Delila search * program. * If you use this searchp with the bacteriophage lambda genome, * J02459, you should find exactly 5 EcoRI sites. * Search can be run from the command line. There is more help * once you start it by typing '?'. You can also run it like this: * * search < searchp * Note: The first line is ignored by the search program! Comments are * lines started with '*'. Help is in the above web page and by '?'. *********************************** begin the search: * Turn on Delila instruction generation (searchinst file) * for the located sequences: D * At this point you can set the range of the instructions * if you don't like the default values. * This sets the 'from' range to 10 bases before the search point: f -10 * This sets the 'to' range to 20 bases after the search point: t +20 * quit the Delila subsystem: q * You can extract the found features using the searchinst file * as the instructions for Delila (move or copy it to the name 'inst'). * Things in quotes turn on the feature generation (searchfeatures file). * There cannot be spaces in the name given in quotes, use underscore * instead, as in "my_search". The searchfeatures is used by * appending it to other material in a features file for the lister * program. * Make the next search be colored in a lister map: C H 0.3 0.5 1.0 1.0 * give the name "EcoRI" * The search is for the sequence 'gaattc': g^aattc * The '^' will mark the cut point of the enzyme. * More enzymes are listed in the 'enzyme' file. * quit the program: q