1Genetics Computer GroupGCGSequence Analysis SoftwareInitialize GCG Programsw analyze% source /disk00/gcg/gcgstartupw analyze% gcg• Usually placed in .login fileGCG BannerWelcome to the WISCONSIN PACKAGEVersion 9.1 -UNIX, September 1997Installed on osfCopyright 1982 -1997, Genetics Computer Group, Inc. a wholly owned subsidiary of Oxford Molecular Group, Inc. All rights reserved.Published research assisted by this software should cite: Wisconsin Package Version 9.1, Genetics Computer Group (GCG), Madison, Wisc.GCG Banner...Databases available:GenBank Release 105.0 ( 2-98)EMBL (Abridged) Release 53.0 (12-97)PIR-Protein Release 55.0 (12-97)SWISS-PROT Release 35.0 (11-97)SP-TREMBL Release 5.0 ( 1-98)PROSITE Release 14.0 (11-97)Restriction Enzymes (REBASE) ( 2-98)GCG Banner...GCG Web Documentation: http://genome.microbio.uab.eduUsername: gcg Password: uabGCG Technical support at UABElliot Lefkowitz: (205) 934-1946; [email protected] Technical support: phone (608) 231-5200 or e-mail [email protected] help: analyze% genhelp or http://www.gcg.com-genhelp/Helpw analyze% genhelp• Online help arranged by programw analyze% genmanual• Online Manualw http://genome.microbio.uab.edu• User’s Guide• Program Manual• Guide to GCG Data2Running Programsw Type the name of the program• No spaces in the program name• lowercase• mapsort• setplotBrief Program Descriptionanalyze% mapsortMapSort finds the coordinates of the restriction enzyme cuts in aDNA sequence and sorts the fragments of the resulting digest by size.MapSort can sort the fragments from single or multiple enzymedigests.Command Line SyntaxMinimal Syntax: % mapsort [-INfile =]GenBank:SynpBR322 -DefaultCommand Line Switchesw Enter at the command line• Switch name entered after a hyphen• -Infile=w Enter on the command line following the program namew Enter at the program promptw Case usually not importantRequired parametersw The program will prompt you and offer a default answerw The -Default switch automatically accepts all default answersPrompted ParametersPrompted Parameters:-BEGin =1 -END=4361 range of interest-CIRcular treats chosen range as circular-ENZymes=*,[.,.,.] enzymes to be mapped-OUTfile=synpbr322.mapsort output file name3Answer the Questionsw Default prompts• (* Yes *)• Accept by hitting return• Change by typing in another response and then hitting returnMapSortanalyze% mapsort(Linear) MAPSORT of what sequence ? vi:vsvcgBegin (* 1 *) ?End (* 11161 *) ? 1000Select the enzymes: Type nothing or "*" to get all enzymes. Ty pe "?"for help on which enzymes are available and how to select them.Enzyme(* * *):What should I call the output file (* vsvcg .mapsort *) ?Mapping ................analyze%mapsort -checkanalyze% mapsort -checkMapSort finds the coordinates of the restriction enzyme cuts in aDNA sequence and sorts the fragments of the resulting digest by size.MapSort can sort the fragments from single or multiple enzymedigests.Minimal Syntax: % mapsort [-INfile=] GenBank:SynpBR322 -DefaultPrompted Parameters:-BEGin=1 -END=4361 range of interest-CIRcular treats chosen range as circular-ENZymes=*,[.,.,.] enzymes to be mapped-OUTfile=synpbr322.mapsort output file nameInput file(s)w Sequence file(s)• Can enter on command line following the program namew Data file(s)Entering Sequence Namesw One sequencew Multiple sequences• File of sequence names• List File• Wild Card• msf File• rsf fileOutput file(s)w -outfile=filenamew Use an extension that identifies the program used to generate the data4Program specific parametersw Sequence information• Begin; End; Strandw Enzyme listw Program variables• Values used in determining results• Window or word size; StringencyData Filesw Restriction Enzyme tablew Translation tablesw Symbol comparison tablesw Amino acid properties• hydrophobicity• charge• Molecular weightw RNA free energy valuesLocal Data Files:-DATa =enzyme. dat restriction enzyme names and recognition sites-DATa =proenzyme.dat peptidases and peptide cleavage reagents-TRANSlate=translate.txt contains the genetic codeLocal Data Filesw Create your own data file to use in place of the one supplied by GCGw Fetch a copy of the GCG filew Edit the file for your own purposes• Must maintain the proper syntax• Each file explains the necessary syntaxw Specify the new file as input to the programLocal Data Filesw analyze% Fetch Enzyme.dat• Get a copy• Modify• Use with the program• -Data=MyEnzyme.DatOptional Parameters - MapSort5Optional Parameters:-ONCe shows enzymes that cut only once-MINCuts=2 shows only enzymes that cut at least 2 times-MAXCuts=2 shows only enzymes that cut no more than 2 times-EXCLude=n1,n2 suppresses enzymes that cut between bases n1 and n2-DIGest sort the cuts for all the enzymes together in one digest-LINear treats chosen range as linear (default)-ALL does an "overlapping -set" map-PERFect looks only for perfect matches-NOSIZe suppresses the report of fragment sizes in your output-MISmatch =1 finds potential sites with one or fewer mismatches.-SILent finds translationally silent potential restriction sites-PLAsmid makes output suitable for display by PLASMIDMAP-FRAGments puts "blocks" not "ticks" into the PLASMIDMAP label file-APPend appends enzyme file and translation table to your outpu t-CUTters[=fn] writes enzyme data file with enzymes that did cut-NONCUTters[= fn] writes enzyme data file with enzymes that did not cut-EXCUTters[=fn] writes enzyme data file with enzymes that were excluded-MINSitelen=6 selects enzymes with 6 (or more) bases in recognition site-OVErhang =0 selects only blunt-end cutters ("5" for 5', "3" for 3')Add what to the command line ?Optional Parameters - MapPlotanalyze% mapplot -check vi:vsvcgMapPlot displays restriction sites graphically. If you don't have aplotter, MapPlot can write a text file that approximates the graph.Minimal Syntax: % mapplot [-INfile=] GenBank:SynpBR322 -DefaultPrompted Parameters:-BEGin=1 -END=4361 the range of interest-ENZymes=*[,...] the enzymes to displayLocal Data Files:-DATa =enzyme. dat restriction enzyme names and recognition sites-DATa =proenzyme.dat peptidases and peptide cleavage reagents-TRANSlate=translate.txt the genetic code-MARk