Question: How To Annotate A Human Dna Position
2
gravatar for Free Man
8.1 years ago by
Free Man170
Earth - China
Free Man170 wrote:

If I know a human DNA position and its code, for example: an "A" located in chr1:207510596-207510597(forward srand), how do I map this location to biological annotation.
And I just want to know what kind of region does this position locate and its possible mutation type: Does it locate in intron, exon or non-coding region, and is it a missense, synonymous or slient mutation?
Is there such a batch mapping tool?
Thank you!

variation mutation dna • 2.1k views
ADD COMMENTlink modified 8.1 years ago by Yuyin11010 • written 8.1 years ago by Free Man170

Do you want a web-based solution, or ready-made tool, or are you willing to do a little programming?

ADD REPLYlink written 8.1 years ago by Neilfws48k

OK, I will develope such a program myself!

ADD REPLYlink written 8.1 years ago by Free Man170
5
gravatar for Chris Miller
8.1 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

You might try snpEff or Ensemble's Variant Effect Predictor

ADD COMMENTlink written 8.1 years ago by Chris Miller21k
3
gravatar for Swbarnes2
8.1 years ago by
Swbarnes21.5k
Swbarnes21.5k wrote:

ANNOVAR can take a vcf file, and maybe some other formats, and return gene annotation, at least for the most common species.

ADD COMMENTlink written 8.1 years ago by Swbarnes21.5k
2
gravatar for Gjain
8.1 years ago by
Gjain5.4k
Munich, Germany
Gjain5.4k wrote:

how about UCSC genome browser.

ADD COMMENTlink written 8.1 years ago by Gjain5.4k
1
gravatar for Yuyin110
8.1 years ago by
Yuyin11010
Yuyin11010 wrote:

You can use UCSC find the annotion region, find the intron, exon or non-coding region, then confirm your location in which region.

ADD COMMENTlink written 8.1 years ago by Yuyin11010
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