Dear Katya, Unfortunately, there isn't an easy way to get the data and format you want in bulk. Here is a way you can get each of the components of the data (coordinates, lod score, sequence) if you have a list of genes in mind that isn't too long.
There are three parts to these instructions. They all use the table browser which you can get to by clicking on tables from the navigation bar. Part 1 (This will give you a list of genes with their coordinates) 1) Set clade: "Insect" 2) Set genome: "D. melanogaster 3) Set assembly: "Apr. 2006" 4) Set group: "Genes and Gene Prediction Tracks" 5) Set track: "FlyBaseGenes" 6) table: "FlyBaseGene" 7) identifiers: if you have a list of gene identifiers you can paste them in here 8) Set output format: "selected fields from primary and secondary tables" 9) If you want the output to go to a file the put the name in the output file: input box 9) Click on "get output" 10) In "Select Fields from dm3.flyBaseGene" check name, chrom, strand, txStart, and txEnd 11) Click on "get output" Part 2 (This will give you a list of genes with their sequences) 1) Set clade: "Insect" 2) Set genome: "D. melanogaster 3) Set assembly: "Apr. 2006" 4) Set group: "Genes and Gene Prediction Tracks" 5) Set track: "FlyBaseGenes" 6) Set output format: "sequences" 7) If you want the output to go to a file the put the name in the output file: input box 8) Click on "get output" 9) Select: "genomic" 10) Click on "submit" 11) Select the sequence retrieval region and formatting options that you are interested in 12) Click on "get sequence" Part 3 (This will get you the lod scores using the gene coordinates that you got from Part 1) 1) Set clade: "Insect" 2) Set genome: "D. melanogaster 3) Set assembly: "Apr. 2006" 4) Set group: "All Tables" 5) Set track: "phastConsElements15way" 6) Click on "define regions" 7) From part one you have a list of coordinates for the genes that you are interested in. You will need to put in those coordinates according to the instructions. If you have a long list of genes you will need to download the "phastConsElements15way" table from our downloads site: http://hgdownload.cse.ucsc.edu/goldenPath/dm3/database/phastConsElements15way.txt.gz and parse the information yourself. 8) Set output format: "selected fields from primary and secondary tables" 9) Select chrom, chromStart, chromEnd, and name. 10)Click on "get output" Please contact the mailing list if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Katya Mkrtchyan" <[email protected]> To: [email protected] Sent: Monday, August 16, 2010 6:18:31 PM GMT -08:00 US/Canada Pacific Subject: [Genome] Question about Genome Browser data Dear UCSC Genome Browser Representative, I am trying to generate the conservation score matrix for all the genes of Dorosophila Melanogaster species. I need following information for all of the genes e.g. for the Gene "Or1a", possition "207,156-208,590", and the lod score "lod=73" following information http://genome.ucsc.edu/cgi-bin/hgc?hgsid=167612178&g=htcGetDna2&table=phastConsElements15way&i=lod%3D73&o=207104&l=207104&r=207177&getDnaPos=chrX:207,105-207,177&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA <http://genome.ucsc.edu/cgi-bin/hgc?hgsid=167612178&g=htcGetDna2&table=phastConsElements15way&i=lod%3D73&o=207104&l=207104&r=207177&getDnaPos=chrX:207,105-207,177&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA> For Or1a gene and the specified possition I need this information(as in the link) for all the lod scores And overall I need this entier information for all genes (e.g. Or1a, Or2a, Or7a...) Is there anyway to have it? Or maybe you have all that information in your servers already saved? Or maybe you can give me some advise to getter that information more quickly? Thank you very much, Katya _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
