Hello Tar, You are correct: we do not compile any utilities for the Windows OS. It is possible to compile isPCR yourself on Windows using something like Cygwin (http://www.cygwin.com/). If you choose to do that, you will need to download the Genome Browser source code:
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip and follow the build instructions in src/product/README.building.source (aslo available here: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source;hb=HEAD). Here is a previous discussion on this list pertaining to building isPcr on Cygwin that you might find helpful: https://lists.soe.ucsc.edu/pipermail/genome/2010-July/022975.html https://lists.soe.ucsc.edu/pipermail/genome/2010-July/022968.html -- Brooke Rhead UCSC Genome Bioinformatics Group On 10/6/11 9:32 AM, Tar Viturawong wrote: > Hello Luvina, > > Many thanks for your speedy response! The table query is exactly what I was > looking for, thank you! > > Unfortunately I only saw that isPCR is only available for linux and not for > windows. Is that the case or did I look in the wrong place? > > Kind regards, > > Tar > >> >> On Wed, Oct 5, 2011 at 9:32 PM, Luvina >> Guruvadoo<[email protected]>wrote: >> >>> Hi Tar, >>> >>> To answer your first question, yes, there is a way to make a batch DNA >>> sequence query. The Table Browser is a useful tool for doing this. From >>> main page, click on "Tables" on the top blue navigation bar. After >>> selecting a clade, genome, and assembly of your choice, set the following: >>> >>> group: Genes and Gene Prediction Tracks >>> track: choose a gene prediction track you would like to use (I'll use >>> 'UCSC Genes' for this example) >>> table: the default table will be the primary table for that track >>> ('knownGene' in this case) >>> region: click on 'define regions', then paste in or upload a file with >>> your coordinates, click 'submit' >>> output format: sequence >>> output file: enter a file name to save your results to a file, or leave >>> blank to display results in the browser >>> >>> Click 'get output'. On the following page, select 'genomic' then click >>> 'get output'. Select any additional options, then click 'get sequence'. >>> For more information on how to use the Table Browser, please refer to >>> our help pages: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html >>> >>> For your second question, there is a utility for batch PCR queries >>> located in the kent source tree. You can download in silico PCR (isPCR) >>> and other utilities here: http://www.soe.ucsc.edu/~kent/exe/. If you run >>> 'isPCR' without any arguments, you will see the usage statement. >>> >>> I hope this information is useful and answers your questions. Feel free >>> to contact us again at [email protected] if you have any additional >>> questions. >>> >>> Regards, >>> --- >>> Luvina Guruvadoo >>> UCSC Genome Bioinformatics Group >>> >>> >>> On 10/5/2011 1:56 AM, Tar Viturawong wrote: >>>> Hello, >>>> >>>> I'm wondering whether there is a way to make >>>> >>>> 1) a batch genomic DNA sequence query (supplying multiple genome >>> coordinates >>>> simultaneously) >>>> 2) a batch *in silico* PCR query (supplying multiple primer pairs >>>> simultaneously) >>>> >>>> without having to actually download the whole genome? >>>> >>>> Many thanks for your help! >>>> >>>> Tar >>>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> >> >> >> -- >> Thanatip Viturawong >> Dept. of Proteomics and Signal Transduction >> Max Planck Institute of Biochemistry >> Am Klopferspitz 18 >> D-82152 Martinsried (near Munich) >> Germany >> +49 1515 6139462 >> >> -- >> Thanatip Viturawong >> Composer/Pianist >> http://tarviturawong.co.uk >> http://youtube.com/pianoinspiration >> > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
