Dear all, The information below is from UCSC genome browser mailing list and it was useful for me. So I post it in this mailing list because first I asked a question to the BioC mailing list, thinking that there was a package to do what I wanted. So here it is the answer to my question: ________________________________ De: Enviada: s?b 16-12-2006 18:37 Para: Ann Zweig Assunto: RE: [Genome] EST?s mapped to a known structural variation region Hello Jo?o, There is a Structural Variation track on the previous human genome browser (hg17, May 2004). You can create a custom track with the data from your experiment, then use the Table Browser to intersect your custom track with the Structural Variation track. I will use these three ESTs as an example to show you how to do this: BI549060 chr7:115495968-115496505 BX098195 chr7:115517846-115520200 AA528379 chr7:115570816-115571048 First create a custom track with the ESTs. 1. Open the hg17 browser and press the "add custom track" button. 2. Add your data as a custom track in a BED4 format like so: track name=ESTs description="ESTs from my microarray experiment" browser position chr7:115493217-115580399 chr7 115495968 115496505 BI549060 chr7 115517846 115520200 BX098195 chr7 115570816 115571048 AA528379 Now use the Table Browser to intersect your custom track with the Structural Variation track. 3. Set up the Table Browser options like so: group = Custom Tracks track = ESTs (or your Custom Track name) region = genome 4. Intersect your Custom Track with the Structural Variation track: press the "create" button next to 'intersection'. Choose: group = Variation and Repeats track = Structural Var table = Tuzun Fosmids (or whichever data table is most appropriate for your interest). Press "submit" to return to the main Table Browser page. Now choose your output type. If you choose BED, for example, you will get a BED list of all of your original ESTs that intersect with the Tuzun Fosmids table. The output in this example is: chr7 115517846 115520200 BX098195 I hope this is helpful to you. Feel free to write back if you have more questions. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu <http: genome.ucsc.edu=""/> Jo?o Fadista wrote: > Dear all, > > I have made a microarray experiment with some EST?s (expression sequence tags) and I would like to see if those EST?s are in a known region of structural variation in the human genome. > > So I was wondering if there is a way, using the UCSC table browser or other application, to input all my EST?s ( their sequence in FASTA format or their positions in the genome) and then retrieve an output file with those that are mapped to a known region of structural variation. > > > Best regards > > Jo?o Fadista > Ph.d. student > > > > Danish Institute of Agricultural Sciences > Research Centre Foulum > Dept. of Genetics and Biotechnology > Blichers All? 20, P.O. BOX 50 > DK-8830 Tjele > > Phone: +45 8999 1900 > Direct: +45 8999 8999 > E-mail: Joao.Fadista at agrsci.dk <mailto:joao.fadista at="" agrsci.dk=""> > Web: www.agrsci.org <https: djfpost.agrsci.dk="" exchweb="" bin="" redir.a="" sp?url="&lt;a href=" http:="" www.agrsci.org="" "="" rel="nofollow">http://www.agrsci.org/"> > ________________________________ > > News and news media <https: djfpost.agrsci.dk="" exchweb="" bin="" redir.asp="" ?url="&lt;a href=" http:="" www.agrsci.org="" navigation="" nyheder_og_presse"="" rel="nofollow">http://www.agrsci.org/navigation/nyheder_og_presse"> . > > This email may contain information that is confidential. Any use or publication of this email without written permission from DIAS is not allowed. If you are not the intended recipient, please notify DIAS immediately and delete this email. > > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome