Hello Hernando, There are a few options for you:
1) Use the Table browser for the batch query, possibly in combination with Galaxy to perform full intersections. The intermediate mapping tables could be the Conservation track or the Chain/Net tracks between Human and Mouse. 2) Download the text files representing the tables in the database for the datasets in #1, then create scripts to process your query. Tools from the UCSC utility set may be helpful. 3) Use the public mySQL server to gain directly access to the database and use mySQL, utilities from our source tree, your own tools, etc. to process the query. 4) Create a local mirror of the Browser and do the same as #3, but locally in your own instance. Do you have a preference? #4 would be the most private option, if that is a concern for you, but would require the most up-front work and may not be necessary. Please write back and let us know your preference and we can send full details about suggested tables & utilities, file download/ftp help, and mirroring assistance. Thank you, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/16/10 8:10 AM, Ernando Faddeev wrote: > I want to compile a list of conserved protein coding transcripts(/genes) > between mouse (mm9<http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm9>) and > human(hg19) that are involved with DNA repair. Basically I want the table > with names next to aligned sequences of the transcripts. I have the names > and accession numbers of around 300 human genes that I am interested in, and > now I want to find the sequences of their mouse homologous. GBrowser appears > to do so in some extend, though only gene by gene and graphically. I have > the required computational skills required to install the database and > manage scripts, though I do not know where to start and what tools to use, > so therefor the question: what tools can I use to build this DB? > > Greetings, > Hernando Sanchez > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
