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
>>
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>>
>> _______________________________________________
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>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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