Hello Tapas, The "Get DNA in Window" tool is 1-based. Almost everything you see in the Genome Browser is 1-based. Only when you use the Table Browser to examine the contents of the tables directly will you see that the smaller coordinate is one base less than the actual coordinate of the item, and the larger coordinate is exactly the same (this makes the internal calculations performed by the Genome Browser much simpler).
For this particular case, hsa-mir-216a, the item resides at chr2:56069589-56069698, on the negative strand. If you hit the "DNA" link at the top of the page, choose the "Reverse complement (get '-' strand sequence)" box, and choose to "Add extra 10 bases upstream (5')", you will get DNA for the range chr2:56069589-56069708. You do not need to adjust anything by one. If you choose to get DNA from the positive strand, you do not need to adjust the coordinates then, either. I would like to suggest another, perhaps easier, way to get the upstream sequence for your miRNA, especially if you have several of them to work with. In the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), make all of the same selections as you describe in your original message, except set "region: genome". Then, enter the name(s) of your miRNAs in the "identifiers (names/accessions)" section. Select "output: sequence". On the next page, you will have the option to "pad" your sequence with any number of "Promoter/Upstream" bases. Using this method, you will not need to adjust any coordinates, and the strand will be determined automatically. I hope this helps get the information you need. -- Brooke Rhead UCSC Genome Bioinformatics Group ----- "tapas bhadra" <[email protected]> wrote: > Respected Sir, > There are 2 options to know the locations of miRNA. > Second > one is -> i) goto > http://genome.ucsc.edu/cgi-bin/hgGateway, (ii) put clade: > Mammal, genome: Human, assembly: Mar. 2006 (NCBI36/hg18), > position: genename (user input), gene: blank, image width: > 800(default). > For example if we give the input miRNA -> hsa-mir-216a, > then > it will show the output as chr2:56,069,589-56,069,698. So if > we need the 10 kbp upstream sequences of this particular > miRNA from > http://genome.ucsc.edu/cgi-bin/hgc?g=getDna&i=mixed&c=chr6&l=999&r=1500&db=hg18 > then what will I give as input? Is it > chr1:56,059,589-56,069,588 or chr1:56,059,590-56,069,589 or > else ? Basically I want to know particularlly whether "Get > DNA in window" is 1 base or 0 base? Pls. explain it for +ve > strand as well as -ve strand. > > Thanking you, > Tapas Bhadra > > > > Hello Tapas, > > > > These methods are extracting data from two sources. One is the > backend > > data table, the other the browser display. Coordinates in the data > table > > use a "0-based" start position - add +1 to get the "1-based" start > > position, as described in this FAQ: > > > > Database/browser start coordinates differ by 1 base > > http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 > > > > When examining data aligned to the reverse strand, the coordinates > in > > the data table are still organized smallest->largest genome > coordinate. > > Meaning, the stop (smallest coordinate) will have the +1 added. This > can > > be a bit confusing, but if you are interested in the details, this > > additional FAQ can be helpful to review: > > > > Coordinate Transforms > > http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms > > > > Please feel free to contact the mailing list support team again if > you > > would like more assistance. > > > > Warm regards, > > > > Jen > > UCSC Genome Browser Support > > > > On 8/3/10 11:36 PM, [email protected] wrote: > >> Respected Sir, > >> I am a research fellow at Indian Statistical Institute, > >> Kolkata, > >> India. I am currently involved in Bio-informatics research. > >> Currently I am searching for chromosomal location of microRNAs. > >> > >> I have found that there is two ways that gives the > desired > >> information. First way to find required information is -> (i) > >> goto http://genome.ucsc.edu/cgi-bin/hgTables , (ii) put clade : > >> Mammal, genome : Human, assembly : Mar. 2006 (NCBI36/hg18), > >> group: Genes and Gene Prediction Tracks, track : sno/miRNA , > >> table: wgRna . > >> Second one is -> i) goto > >> http://genome.ucsc.edu/cgi-bin/hgGateway, (ii) put clade: > >> Mammal, genome: Human, assembly: Mar. 2006 (NCBI36/hg18), > >> position: genename (user input), gene: blank, image width: > >> 800(default). > >> > >> For example : miRNA - hsa-mir-216a > >> 1st one gives : chr = 2 , chromStart = 56069588 chromEnd = > 56069698 > >> 2nd one gives: chr2:56,069,589-56,069,698. > >> > >> But the 2 ways gives everything right except chromStart. > If > >> first one gives its value equal to x then second one gives its > >> value equal to x+1. Please give me the information regarding > >> which one is correct > >> > >> Thanking you, > >> Yours > faithfully, > >> Tapas Bhadra > >> Senior Research > >> Fellow, > >> ISI Kolkata > >> > >> This mail is scanned by Ironport > >> > >> > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > This mail is scanned by Ironport > > > > > > > This mail is scanned by Ironport > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
