Hello Anil, When using the option of output = sequence, the type of sequence and the regions of those sequence available for output depend on the type of underlying data in the track. The track description for any data set will contain information about the source, methods, credits, and sometimes additional help links to external sources of information. To find a track's description, open the browser for the target assembly and click on the track's name.
For data tracks in the Gene and Gene Predictions group, many will have the sequence output options of genomic, mRna and protein. A few will have limited options such as genomic sequence only. For data tracks in the EST and mRNA group, the option will always be genomic sequence. There is no list for each track - instead bring up the track in the Table browser to see the options provided. To do this, using the Table browser, select the track you wish to retrieve sequence from and leave the default, primary table selected. Then, for output format, select "sequence". Next, name the file (for download) and submit the query using the "get output" button. The following series of forms will reflect the types of sequence data available, including in many cases the option to specify regions. Again, the forms/options presented is variable and dependent on the track contents. The final submit from these form(s) will return the sequences in fasta format. Sequence types: genomic = the region of the reference genome covered by the aligned sequence from the track mRNA = the actual aligned mRna sequence from the track protein = an associated protein derived from or linked to the aligned sequence from the track Sequence regions: For tracks with an mRNA sequence offered, with a defined coding region, specific regions of that mRNA sequence can be chosen: 5' UTR, CDS (coding region), 3' UTR and upstream/downstream regions. These regions, including the 3' UTR, are based on the evidence associated with the track contents. mRNA example: RefSeq - the coding region is defined in the files from Genbank, those coordinates are linked into the track, and the resulting 3' UTR region's confirming evidence is from the source (RefSeq/Genbank). For tracks with a genomic sequence offered, without a defined coding region or only a coding region, there is no options for a 5' UTR or a 3' UTR, since is not contained in the track contents. Instead, the option to retrieve genomic data upstream or downstream will often be offered as a substitute. Table browser help links: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Sequence Hopefully this helps to explain the data, but please let us know if you have a specific track or sequence type/region that you would like more clarification about, Thank you for you patience while we created your reply, Jen --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/30/10 7:37 AM, Anil Kesarwani wrote: > Dear Sir/Madam: > > I am using UCSC Table browser to extract Human and Yeast 3' UTR sequences. I > got a bit confused with the multiple options given in the Table Browser. > Will please guide me in this regards. Also, I would like to know how the > experimental evidences supporting 3' UTR annotation. > > I would highly appreciated for you kind response. > > Thanking you. > > With regards, > Anil Kesarwani > ============================== > Anil Kumar Kesarwani > Research Scholar > > Centre for Molecular Biology of Plants > Department of General Genetics > Eberhard Karls University > 72076 Tuebingen, Germany > > Work: +49-(0)7071-2976147 > Mobile: +49-(0)17624957493 > ============================== > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
