PCFOLD 4.0 DOCUMENTATION To use this software you need: -IBM PC, XT, or AT or compatible -512 Kbyte of RAM minimum -Floppy 360 Kbyte or floppy 1.2 Mbyte -DOS 2.0 or later version -To work properly, this program will need the ANSI.SYS to be installed by adding the command DEVICE=ANSI.SYS to the CONFIG.SYS file. This diskette contains two versions of PCFOLD. The first one, called PCFOLD.EXE, is a version that packs the arrays, to extend the length of the longest fragment (425 base maximum) it can fold. The second version, called PCFOLD2.EXE, does not contain packing and can handle only fragments of 345 bases. To run the first one type PCFOLD, and to run the second one type PCFOLD2. Neither program requires a math coprocessor chip. ============================================================================== Upgrade info: Version 4.0 1) Energy model of Turner et. al. (Cold Spring Harbor Symp. Quant. Biol. Vol 52, 123-133, (1987)). 2) Accepts longer file names (i.e. path names). 3) "Friendlier" help files, Auxiliary info descriptions and file queries. 4) Accepts upper/lowercase Y/N. 5) No floating point math in either routine. 6) Includes separate program to change temperature of energy files The energy model of Turner et. al.(1987) improves the prediction of RNA secondary structure due to both additional measured paramters and changes in the program For example (see reference above): % Helices predicted with the data set of.. RNA Salser Turner et. al. ------------------------------------------------------------------------ tRNA 69 92 5S 45 67 EColi 16S Domain 1 8 46 " Domain 2 53 60 " Domain 3 14 55 " Domain 4 0 75 " summary 20 54 Group I intron from 50 79 T. thermophilia PCFold 4.0 includes the changes made to the original RNAFold program to give these results. The changes are a penalty for asymmetric internal loops, as suggested by Ninio (Papanicolaou et.al. Nucleic Acids Res. 12, p.31(1984)), and a different way of treating GU base pairs. 1) Asymmetric internal loops AAAAAAA AAAAA ...GG AG... ...GG AG... ...CC UC... ...CC UC... AAA---- AAAAA asymmetric internal loop symmetric internal loop PCFold 3.0 considered these equally destablizing; PCFold 4.0 makes the asymmetric internal loop more destablizing. 2) GU pairs. In previous versions of RNAFold and PCFold, GU pairs were not allowed at the ends of helices (closing off a hairpin or an internal loop, for example), and GU and UG nearest neighbors were considered the same. For example, GC UC UG and GG had the same free energy. In PCFold 4.0 GU pairs can end helices, and the GU and UG nearest neighbors are different. John Jaeger Bitnet: dhtu@uordbv Internet: dhtu@db1.cc.rochester.edu ============================================================================== This diskette contains the following files: README.DOC This file. PCFOLD.EXE Packed version of PCFOLD. Can fold up to 425 bases. PCFOLD2.EXE Version without packing of the arrays. Can fold up to 345 bases. MENUDAT2 | Data files needed by the program. MENUDAT | MSG.HLP | csh37.ENR default Energy file. PSTV Default sequence file. QBETA.PC | Two other sequence files TTHERMOP.PC | NT.EXE | Collection of files that let you change the temperature NEWLOOPS.DAT | of the energy file. csh37.enr is set for 37 C. Look NEWTEMP.BAT | at NEWTEMP.DOC for more information. NNNEW.DAT | NEWTEMP.DOC | SEQ.DOC | How to set up a sequence file. MOLECULE.COM | Program and routines needed for then MOLECULE MOLECULE.PAS | secondary structure plotting program. MOLECULE.HGC | MOLECULE.IBM | INSTALL.BAT | <- installation routine for IBM vs. Hercules graphics *.FON | Note: Zuker Sources Have been deleted from this working disk to make room for graphics display routines (described below). ************************************************************************ PROGRAM MOLECULE : GRAPHIC DISPLAY OF PCFOLD GENERATED STRUCTURES J. Ryan Thompson Dept. of Biol. Sciences Carnegie-Mellon University Pittsburgh, Pa. 15213 412-268-3412 The program MOLECULE reads a .CT file produced by Zuker's PCFOLD program and displays a 2D representation of the structure. Hardware Note: The Graphics procedures on this Disk are initially configured for a Hercules (monochrome) Graphics card. To Reconfigure for IBM color or Hercules hardware, Insert Disk into Drive A:, Log onto Drive A: and type "INSTALL". Example Secondary Structure Analysis Procedure: A>PCFOLD ***** Start Interactive Zuker Program. ***** Note: MUST Answer "YES" to .CT file prompt. A>MOLECULE anyname.CT ***** Draw the structure defined by ANYNAME.CT ***** Hit Any key to erase the Graphic. OPTIONAL PARAMETERS Three optional parameters may be used to modifiy the display: /B : Draw the Backbone of the Structure /D : Draw the Structure with Dots /T : Include a Title on the Graphic examples: A> MOLECULE anyname.CT /D A> MOLECULE anyname.CT /T A> MOLECULE anyname.CT /D /B A> MOLECULE anyname.CT /B A> MOLECULE anyname.CT /B /D /T Parameters may be in any order but must follow the .CT filename. A Documentaion Screen is obtained by typing MOLECULE with no filename or parameters. OVERLAPPING STRUCTURES (Angle Corrections) The angle that stem leave a loop can be adjusted to prevent overlaps. Angle correction Data is placed in a .AGL file (i.e. for the structure described by the file SNR119.CT, the filename SNR119.AGL must be used to store the angle corrections. To create the .AGL file, use any editor capable of generating a standard ASCII file. Angle corrections consist of 1 line each containing 2 integers: the nt Position and an angle to rotate the stem. Make angle corrections at positions corresponding to the base of a stem ONLY. Example .ANG File: 95 15 ***** Rotate the stem beginning nt 95 by +15 degrees. 45 -10 ***** Rotate the stem beginning nt 45 by -10 degrees. 0 ***** End of angle corrections. Note: The /D option is recommended while making angle corrections as each 10th nucleotide is displayed with an open symbol. Acknowledgements: The original Molecule program was provided by Dr. Robert Cedergren (Lapalme, Cedergren, and Sankoff NAR 10:8351-8356(1982)). The machine dependent graphics functions were isolated in a separate procedure, translated into Turbo Pascal 3.0, and modified to accept input from Zuker's FOLD program by JRT. Turbo Graphix Tool Box procedures (Borland) were employed to display the image. The original MOLECULE program was written in Pascal 6000 at the Univ. of Montreal. The version of Molecule included here is still under development but is quite functional. Currently, two intermediate text files are generated by the molecule program (temp.mol and temp.xtd). This cumbersome approach is really only a temporary solution resulting from combining several modules that functioned as separate programs into a single program. The user need not be aware of these files except to realize that some free disk space on the default Drive is required. Of course, Speed of execution would be increased if the data were passed between procedures instead of written to disk. Another improvement I envision is a procedure to move a cross-hair over the graphic in order to select the position(s) for an angle correction. The source code (MOLECULE.PAS) is included here so others may attempt these improvements if desired. Please send improvements to J. Thompson. p.s. A known bug causes a System Crash if you attempt to print a graphic while the printer off line.