loopDloop is a software tool for drawing RNA secondary structures in molecular biology. There is one version written for Macintosh computers (see folder mac-app/). There is another verison written in the Java language for any computer that supports that (see folder java/). NOTICE: These are unfinished versions that may be lacking in features or may fail in various ways. LoopDloop is an secondary structure drawing program - it is not an RNA folding program. The base pairings (i.e. secondary structure) are defined by the user, not predicted by the program. LoopDloop then allows the manipulation of the resulting secondary structure representation. loopDloop accepts data in three forms: CT (connect) file format, a file with interleaved sequence and pairing character lines, or the format for Gary Olsen's LOOPSOL program. You can obtain new releases of this software thru anonymous FTP to iubio.bio.indiana.edu, in folder /molbio/loopdloop/, or using HTTP or Internet Gopher to iubio.bio.indiana.edu, in a folder called "IUBio Software+Data/molbio/loopdloop/". Comments, bug reports and suggestions for new features (see below) may be addressed via e-mail to Software@Bio.Indiana.Edu Note for editing large structures: Switch "Loops:Loop Prefs..." dialog choice from the Polygon multiloop to the Arc multiloop, and enable the "Show Ties" checkbox. Ties used to straighten out loops do not work with the Polygon method. History LoopDLoop was started Winter of 1989 as a modern tool with a good user interface, for drawing and editing RNA secondary structure. A preliminary version has been in limited distribution for a few years. A subset of loopDloop, lacking the editing operations, was released as LoopViewer in the Fall of 1990. LoopDLoop has been converted to a MacApp-based program. 8 December 96, version J2.01 - first Java version of the program. Lacking in many of the editting and other features of the Mac-app version. 18 July 94, v 1.2a63 & 1.2a64. The expiration date is removed from the the software. Version a63 is generic Motorola 68000 code, and should run albeit slowly on PowerMacs. Version a64 is Motorola 68020-68040 + Math FPU specific, and will run faster on Macs with those processors. This is likely the last Macintosh-only version as a conversion to the platform-independent framework DCLAP is underway. 4 December 92, v 1.2a61 -- minor update to add the "Hide levels of 2ndry structure" option in the "Loop:Base Prefs..." dialog. This lets you edit large structures more easily by hiding chunks of the tangled spaghetti. Enter a minimum and maximum number, and base pairs outside of those numbers are hidden. The mininum is toward the outside (5' and 3' ends of loops), and the maximum is toward the center of the structure. These numbers are counted from number of base pairings starting from the 5'-3' outside. The best way to untaggle a large structure is to start with levels 0 to 10 or so shown, and the inner levels hidden. Work to straighten out stems extending from the outer loops. Then progressively unhide higher levels, straightening the stem extensions from newly exposed loops as you go. 4 August 92, v 1.2a57 -- First public release of loopDloop.