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DON'T PUT A COMMENT ! -- The seqweb interface to GCG at the HPCf :: --- Acknowledgments This workshop was supported by RCMI Award G12RR-03501 NCRR, NIH BRIN Award P20 RR16470-01 NCRR, NIH HPCf vBNS Award 9976006 NSF/ANIR HPCf VizLab Award 9977805 NSF-EPSCoR Grant The letters A and G, and the number 112 :-) :: ----- this is a comment ---------------------------------------------------- Introduction seqweb is a web browser interface to several of the most common tools for sequence analysis in GCG :: --- Sequence Analysis What is GCG? The Wisconsin Package for Sequence Analysis (gcg) Consists of 130+ integrated programs !hwww.hpcf.upr.edu/biology/gcghelp/short_descriptions.html Currently available at the HPCf Requires a research account on our supercomputer Web based, Command-line and X Window System versions available See !hwww.accelrys.com or !hwww.hpcf.upr.edu/biology/gcg.html :: --- seqweb a web interface to the most often used GCG programs Database Searching and Retrieval Comparison Protein Analysis Mapping Evolutionary Analysis Pattern Recognition and Motif Searching Nucleic Acid Secondary Structure Primer Prediction See !hhttp://www.accelrys.com/products/seqweb/index.html :: --- Why should you use seqweb? GCG is standard A single GCG license supports the entire UPR community seqweb programs are integrated (only submit a sequence once) seqweb data backed up regularly seqweb results saved on server (you can share them, continue processing, ...) :: --- Why shouldn't you use seqweb? Requires a very particular set of web browsers Output is sort of generic, other programs have better looking output Seqweb is not GCG, so many of the 130+ gcg programs are not available Your data is sent to our server and kept there (privacy, confidenciality) You need to acknowledge/cite 4 grants and the company :: --- Requirements Client requirements: Windows PC: Netscape 4.77, 4.78, 4.79, 6.2 or Microsoft Internet Explorer 5.5 or 6.0 Macintosh: Netscape Versions 4.77, 4.78, 4.79, 6.2 or Internet Explorer Versions 5.0, 5.1 UNIX: Netscape Versions 4.77, 4.78, 4.79, 6.2 See: !hhttp://boreas.hpcf.upr.edu/help/recommendations.html :: --- Logging In Fire up the appropriate browser go to !hboreas.hpcf.upr.edu enter your username and password if you don't have one send mail to !mhelp@hpcf.upr.edu :: --- The seqweb Interface Multiple frames inside browser See online documentation from your account: !hhttp://boreas.hpcf.upr.edu/help/getting_started.html#window_desc :: --- Sample Data Download and save these sequences on your computer, we will use them to test seqweb, or bring your own nucleotide sequences. !lhzf3sub3.gbk !lnurr1.gbk :: --- Example analysis comparing two nucleotide sequences Select "Globally align two nucleic..." from the Gap section of the Comparison programs The window will change to the Gap program window, wait for the input sequences box to fully load. This may take several minutes over a dial-up line :: --- Uploading Sequences Select "Local File" button under "Add From" Select !lnurr1.gbk on your local disk. Open !lhzf3sub3.raw, copy to clipboard then select "Clipboard" Click on "Database", then get AF016297 Click on "Refresh" to update the sequence display :: --- Running Gap Click on a sequence summary line to select it Click on another, then try to select a third. Click "Run" or "Run In Background" :: --- Getting Help on Gap Look over the program options, click on the names to get help More help is available in the help link at bottom The Gap manual is available by selecting the book at the top right Other questions may be set to !mhelp@hpcf.upr.edu :: --- Managing and Editing Sequences All sequences submitted are stored on server The sequence manager may be used to select sequences for analysis, or to edit your sequences !hhttp://boreas.hpcf.upr.edu/help/image/seq_mgr_window.gif :: --- Managing Jobs and Results or "Help! Where did my results go?" All analysis results stored on server You don't need to rerun the programs, just review previous results See the results manager (or the job manager if the run isn't finished) !hhttp://boreas.hpcf.upr.edu/help/image/results_mgr_window.gif !hhttp://boreas.hpcf.upr.edu/help/image/job_mgr_window.gif :: --- More Help Full help pages available online within the application !hhttp://boreas.hpcf.upr.edu/help/ (UPR only) Each program also has it's own page. Like !hhttp://boreas.hpcf.upr.edu/help/gap.html :: --- About this presentation The presentation was prepared with slides.sh, available from: !hhttp://fx.lebail.free.fr/slides-latest.tar.gz The presentation is at: !hhttp://www.hpcf.upr.edu/~humberto/slides.sh/seqweb/ The source of the presentation is available here: !lsource.txt