The accompanying zip file (generunr.zip) contains the GeneRunner for Windows demo from Hastings Software: Hastings Software Inc. PO Box 567, Hastings on Hudson, NY, 107106 USA Voice: (914) 969-0855 Fax: (914) 376-4433 email: hasoft@biotechnet.com To use it, first download the zip file to your PC using binary mode FTP. Use pkunzip to unzip the file to a 1.44MB floppy disk (it won't fit on a 1.2MB). It may also work from your hard disk; I haven't tried. Once you have the disk ready, start Windows, if you haven't already, and from the Windows FIle menu, choose RUN and type a: (or b: or whatever device you've chosen) setup and hit return. Answer the questions and have fun. Uploaded by Harry J Mangalam Biocomputing, Salk Institute mangalam@salk-sc2.sdsc.edu with permission from Hastings Software. The following is a horribly mangled version of the Quick Tour that came with it. It purports to be a MS Word for Windows 2 .DOC file but I certainly can't get it to import correctly. However, while you're waiting for the real verison to inch it's way to your door, you can dig thru the text and follow approximately what's going on. The bitmaps on the original helped - but the parenthesized bits indicate what you're suppoed to do. There is a short preview in the current issue of Biotechnology software (April/May, 1993) and a longer review coming next issue (they say). This file is in BINARY format, created by HASOFT at 28-APR-1993 14:03:40.11520 bytes. Checksum = 1912 XCRC = 52CE CRC16 = 921F. [*BINARY*128]~[~%-`x@^I^D``<`-`\'%@^A``w^R``~w,`\._^Q`\?*``$``*``$`$*`\ $*`\ $*`\ $*`\ $*``^N`2*``^R`D*``,`p*`\ p*`\ p*`\ p*``^P`%@*``^J`p*`\ %J*``(`~2*`\ ~2*`\ ~2*`\ ~2*`\ ~2*`\ ~2*`\ ~2*`\ ~2*`\ ~2*``^B`~4*`\ ~4*`\ ~4*``^_`~S*``~@`%S+`\ %S+``^^`%P,``4`~D,``3`~1+``~_`$*`\&~1+`\ ~1+`\"^R`^T`^B`^A`\W A Quick Tour through ^M^JGene Runner^M^J^M^J^IAfter Gene Runner has been started (by double clicking on the DNA Icon), click on the File menu item, then click on "1 snpbr322.seq" at the bottom of the menu list to open the pBR322 sequence. A new window appears with the sequence. Click on the ^A (ORF analysis) button just below the menu. A dialog window appears, with all the options for ORF analysis. Parameters may be adjusted, but the defaults are generally fine. Click on the OK button on the bottom of the dialog. The ORF analysis automatically translates the sequence, then creates a new window containing a list of ORFs. Highlight item number ten in the list by clicking on it (you may need to use the scroll bar to display it in the window). Then, click on the button labeled "GO TO" on the bottom right of the ORF analysis window. The GO TO button automatically highlights the exact range of amino acids in the translated sequence (the GO TO feature is used extensively throughout Gene Runner). Any highlighted region is automatically used as the region for an analysis. ^M^J^IClick on the ^A ( Restriction analysis) button. Note that the region parameters in the bottom right of the restriction analysis dialog automatically contain the base range for the ORF (including the stop codon). Restriction analysis defaults to the "Cut out region" analysis, finding all the enzymes that cut outside of the highlighted base range, that is, if an enzyme cuts outside of the highlighted base range, but also cuts inside of the range, the enzyme is not listed. Click OK to begin the analysis. A new window appears, listing all the enzymes that met the parameters set in the restriction analysis dialog. Click on the "SEL ALL" button on the bottom of the restriction analysis window. This selects all of the enzymes listed in the window for subsequent use. Next, click on the ^A (Fragment analysis) button. The fragment analysis dialog appears, defaulting to a cut out fragment analysis. Click OK. A new window appears listing all the single and double digests that may be used to cut out the ORF that was initially selected. Each digest is listed with relative separation on an agarose gel, giving you an idea of how easy it would be to isolate the fragment. ^M^J^INow lets splice this ORF into lambda. Click on File, then "2 lambda.seq" to open lambda. Click on the Edit menu item, then the GO TO menu item. In the dialog type "20\ -40\ " then click OK. Then click on the restriction analysis button, change the cut out region to cut in region selection, and click OK. Click the Sel All button, then click on the fragment button. This time, the default is a cut in fragment analysis. Click OK. When the analysis is complete click on the ^A (Clone analysis) button. Check the button labeled "OK to partially fill overhangs", then click OK. A Clone analysis window appears listing all the ways to clone the original ORF into lambda between bases 20,000 and 40,000 (in a more realistic example, a cloning vector would be used with a 100 bp range). Select any one of the clones, and click on the "REPORT" button to view/edit the details of the experiment then click OK. Click on the "CREATE" button at the bottom of clone window to create the new sequence. The fragment used from pBR322 is highlighted in the pBR322 sequence window, the fragment used from lambda is highlighted in its window, and the inserted fragment is highlighted in the new sequence. The new sequence will correctly contain the post overhang-modification sequence. Note that the highlighted fragment in the new sequence may indicate different overhangs than the one in pBR322 if the clone required overhang modification.^M^J^ILocate the ORF window (snpbr322.ORF) with the Window menu item. Select the ORF and click on "GO TO". Click on the ^A (PCR analysis) button, then click OK. A list of products with the corresponding sense and anti sense primers is generated. Click on any product, then click on the "GO TO" button. The PCR product is highlighted. Click on the Edit menu item, then the Copy menu item. Click on File, New,Nucleic Acid. Click on Edit,Paste. You now have your PCR product sequence.^M^J^ILocate the pBR322 sequence window, then using the mouse, highlight a small range of bases (20-30). Then click on the ^A oligo button to see a complete oligo analysis of that sequence.^M^J^\~F^B``:`^H`~e^B~e^B`\,~$^A~$^A~h^C~h^C`\2^A`^I``^CF^A`\ "^A`\ ^E```^K^B`\ ^E```^L^B^\`^\`^E```^I^B`\ ^E```^A^B}~{~p`^D```^G^A^C`"^A``C^O `~L```^\`^\`\!^\`^\`\!(```^\```^\```^A`^D`\!~@^A`\4%@``%@```%@%@`%@```%@`%@`%@%@``%@%@%@`~@~@~@```}``}```}}`}```}`}`}}``}}}`\%`\$~x%H\(%@``~x%H\(%@~ww~x%H\(%@~ww~x%H\(%@p`~x`\(%@p`~x^H^H%H%H%H^H^H^H%H%H%H`%@p`~x^H%@%H%H%@%H^H%@%H%H%@%@%@p`~x^H%H``^H%H^H%H``^H%@%@P`~x^H^H%H%H%H^H^H^H%H%H%H`%@r"~x^H%@%H%H%@%H^H%@%H%H%@%@%@p`~x^H%H``^H%H^H%H``^H%@%@P%@~x^H^H%H%H%H^H^H^H%H%H%H`%@r~*~x^H%@%H%H%@%H^H%@%H%H%@%@%@r~*~x^H%H``^H%H^H%H``^H%@%@r"~x^H^H%H%H%H^H^H^H%H%H%H`%@r"~x^H%@%H%H%@%H^H%@%H%H%@%@%@~r"~x^H%H``^H%H^H%H``^H%@%@r"~x^H^H%H%H%H^H^H^H%H%H%H`%@~r"~x^H%@%H%H%@%H^H%@%H%H%@%@%@P`~x^H%H``^H%@^H%H``^H%@%@r"~x%@%H\ ^H%@%H\ ^H%@p`~x%H^H%H%H%@%H%H^H%H%H%@%H%@P`~x%H%@``^H%H%H%@``^H%H%@r"~x%H\#%H\!%@p`~x%H\(%@p`~x%H\(%@x%H}\)~px%H^C`\!%@`~F^B``:`^H`~e^B~e^B`\,~$^A~$^A~h^C~h^C`\2^A`^I``^CF^A`\ "^A`\ ^E```^K^B`\ ^E```^L^B^\`^\`^E```^I^B`\ ^E```^A^B}~{~p`^D```^G^A^C`"^A``C^O `~L```^\`^\`\!^\`^\`\!(```^\```^\```^A`^D`\!~@^A`\.`\"%@``%@```%@%@`%@```%@`%@`%@%@``%@%@%@`~@~@~@```}``}```}}`}```}`}`}}``}}}`\-~x%H\(%@``~x%H%H%O%H\%%@}}~x%H%H%G~x%H\$%@~w^?~x%H%H%G^?%H\$%@x^H~x%H%H%Gw~x%H\#%@x%@~x%H%H%Hw^?%H\#%@~p^H~x%X%H^Qw^?%X%H^Q%H%I%X%H%@x^H~x%I%A%Hw^?%I%A%H^X%X%I%A%@x%@~x%H%Q%Hw^?%H%Q%H%A%X%H%Q%@~p^H~x%H%X%Hw^?%H%X%H%A%H%H%X%@H^H~x%A%I%Hw^?%A%I%H%X^X%A%I%@s~3~x^X%H%Yw^?^X%H%Y%H%A^X%H%@~p^H~x%H%H%Hww~x%H\"%@~x`~x%H%H%Hww~x%H\"%@x%@~x%H%H%Gxpx%H\"%@~p%H~x%H%H%@^H^O^O%H\"%@~x^H~x%H%H^O%@~x%@~x%H\!%@x%@~x%H%H^O%@~x%@~x%H\!%@~p%H~x%H%H^O%@~x%@~x%H\!%@~x^H~x%H%H^O~p~x%@~x%H\!%@x%@~x%H%H%@^H^O^O%H\"%@~@%H~x%H\ %@%H\#%@~{;~x%H\(%@x%H~x%H\(%@~p%H~x%H\(%@~x%H~x%H\(%@x%@}\)~pp`^C`\!P`~F^B``:`^H`~e^B~e^B`\,~$^A~$^A~h^C~h^C`\2^A`^I``^CF^A`\ "^A`\ ^E```^K^B`\ ^E```^L^B^\`^\`^E```^I^B`\ ^E```^A^B}~{~p`^D```^G^A^C`"^A``C^O `~L```^\`^\`\!^\`^\`\!(```^\```^\```^A`^D`\!~@^A`\4%@``%@```%@%@`%@```%@`%@`%@%@``%@%@%@`~@~@~@```}``}```}}`}```}`}`}}``}}}`\-~x%H\(%@``~x%H\ ``%@`^H``%H%@~ww~x%H\!^H%@%H^H^H%@%H%@~ww~x%H\!^H%@%H^H^H%@%H%@p`~x%H\ ^H^H%@%H^H^H%@%H%@p`~x%H\ %@^H%@`^H``%H%@p`~x%H\#%H\!%@p`~x%H\ ^H%@%H%H%@%H^H%H%@P`~x%H\ ^H`%H%H%@^H^H%H%@r"~x%H\ `\"^H%H%@p`~x%H\ ^H`%H%H%@^H^H%H%@P%@~x%H\ ^H%@%H%H%@%H^H%H%@r~*~x%H^Q%H%H^I%H%H^Q%H%H^I%H%@r~*~x%A%H^X%I^H%X%A%H^X%I^H%X%@r"~x^X%H%A%X^H%I^X%H%A%X^H%I%@r"~x%X%H%I^X^H%A%X%H%I^X^H%A%@~r"~x%X%H%I^X^H%A%X%H%I^X^H%A%@r"~x%I%H%X%A^H^X%I%H%X%A^H^X%@~r"~x%H%Y%H%H^A%H%H%Y%H%H^A%H%@P`~x%H\ ^H%H\!^H%H%@r"~x%H\ ^H%H\!^H%H%@p`~x%H\ ^H%H\!^H%H%@P`~x%H\ ^H%H%H%H%H%H^H%H%@r"~x%H\(%@p`~x%H\(%@p`~x%H\(%@x%H}\)~px%H^C`\!%@`~F^B``:`^H`~e^B~e^B`\,~$^A~$^A~h^C~h^C`\(`\&^A`^I``^CF^A`\ "^A`\ ^E```^K^B`\ ^E```^L^B^\`^\`^E```^I^B`\ ^E```^A^B}~{~p`^D```^G^A^C`"^A``C^O `~L```^\`^\`\!^\`^\`\!(```^\```^\```^A`^D`\!~@^A```\2%@``%@```%@%@`%@```%@`%@`%@%@``%@%@%@`~@~@~@```}``}```}}`}```}`}`}}``}}}`\-~x%H\(%@``~x%H%H%H%@```^H%H\ %@~ww~x%H%H%H^H%H%H%H%@%H\ %@~ww~x%H%H%@%H\!^H%H%H%H%@p`~x%H%H^H%H\!%@%H%H%H%@p`~x%H%@%H\#^H%H%H%@p`~x%H%@%H\#^H%H%H%@p`~x%H%@%H\#^H%H%H%@P`~x%H%@%H\#^H%H%H%@r"~x%H%@%H\#^H%H%H%@p`~x%H%@%H\#^H%H%H%@P%@~x%H%H^H%H\!%@%H%H%H%@r~*~x%H%H%@%H\!^H%H%H%H%@r~*~x%H%H%H^H%H%H%H%@%H\ %@r"~x%H%H%H%@```^H%H\ %@r"~x%H\!%@%H\"%@~r"~x%H\!`^H%H\!%@r"~x%H\ %@``%H\!%@~r"~x%H\!%@%H\"%@P`~x%H\!%@%H\"%@r"~x%H\!%@%H\"%@p`~x%@`\&^H%@P`~x%HHH(H((H((H%H%@r"~x%HHH(H((H((H%H%@p`~x%@`\&^H%@p`~x%H\(%@x%H}\)~px%H^C`\!%@`~F^B``:`^H`~e^B~e^B`\,~$^A~$^A~h^C~h^C`\2^A`^I``^CF^A`\ "^A`\ ^E```^K^B`\ ^E```^L^B^\`^\`^E```^I^B````^E```^A^B}~{~p`^D```^G^A^C`"^A``C^O 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