Hello Tommaso, Unfortunately we do not have a simple tool that does what you are describing. The code that creates the display is deeply embedded in the browser. We recommend using custom tracks to display your data as previously described by my colleague.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 06/15/11 02:55, Tommaso Mazza wrote: > Dear Mary, > thank you for your prompt answer. > > We have our own tool (AURA database) and we would like to draw and show, > programmatically, our mRNA structures in terms of exons and introns. In > rpactice, we would like to mimic the same view we have in genome browser > (and that you were correctly suggesting can be downloaded as pdf/ps format). > We were wondering if within the Kent tools or the genome browser API > there is a piece of code or a particular tool that we could > run/integrate into our code to generate these images. > > Thank you very much > > > > On 14/06/2011 19.46, Mary Goldman wrote: >> Hi Tommaso, >> >> I'm not quite sure if I understand your question. If you are looking for >> a pdf of an image that you see on the browser, you can click the PDF/PS >> link in the top blue bar. This will take you to a page where you can >> obtain a pdf of either the browser graphic or chromosome ideogram. >> >> Alternatively, if you have you are trying to visualize the exon-intron >> structure within your own data, I would recommend uploading a custom >> track into our browser. More information on custom tracks can be found >> here: >> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks. I >> believe that you will probably want to build the track in BED format: >> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED. >> >> I hope this information is helpful. Please feel free to contact the mail >> list again if this does resolve your issue or if you require further >> assistance. >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> On 6/14/11 3:09 AM, Tommaso Mazza wrote: >>> Hi, >>> is there any specific software tool that allow to obtain an image of the >>> exon-intron structure of an mRNA, like the one visualized into the >>> genome browser ? Maybe inbetween Kent's collection of tools ? >>> thank you very much >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
