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 > -- 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
