Hi Toril, If you can get the mRNA for your gene, you can use the Human mRNAs Track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr22&g=mrna) to view detailed alignment in the same format as BLAT. This details page for the particular mRNA has a link to the alignment information. Here is an example of a details page with the link:
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=235798735&o=39966757&t=40080533&g=mrna&i=AF211189 Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Vanessa Kirkup Swing <[email protected]> Date: Tue, Jan 10, 2012 at 2:42 PM Subject: Re: [Genome] Get DNA block function To: Fagerheim Toril <[email protected]> Cc: "[email protected]" <[email protected]> Hi Toril, The feature that you are thinking of is part of the BLAT Search results (http://genome.ucsc.edu/cgi-bin/hgBlat). Here is an example of the results page I think you are referring to: http://genome.ucsc.edu/cgi-bin/hgc?o=39996237&g=htcUserAli&i=../trash/hgSs/hgSs_genome_2da_cbc520.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_2da_cbc520.fa+hg19_dna&c=chr22&l=39996237&r=39997074&db=hg19 Hopefully this helps. If you have further comments or questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Fagerheim Toril <[email protected]> Date: Tue, Jan 10, 2012 at 4:14 AM Subject: [Genome] Get DNA block function To: "[email protected]" <[email protected]> ikke sensitiv (for security reasons only- please ignore) Hi I wonder if the block function when retreiving a DNA sequence for a gene is lost or hidden somewhere else. In earlier version, you could get the genomic sequence of your gene in interest with e.g exons in capital letters and the rest in small letters. In the ourput page you then had a left side option of jumping from block to blok, that is from exon 1 to 2 etc. This was very convenient. The output now is a large fasta file where you have to scroll down. Any hints on how to find this? Kind regards, Toril Fagerheim Senior Hospital Scientist University Hospital of North Norway _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
