Question

How To Annotate A Human Dna Position

2

Entering edit mode

12.3 years ago

Free Man ▴ 180

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!

dna mutation variation • 3.1k views

ADD COMMENT • link updated 12.3 years ago by Yuyin110 ▴ 10 • written 12.3 years ago by Free Man ▴ 180

0

Entering edit mode

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

ADD REPLY • link 12.3 years ago by Neilfws 49k

0

Entering edit mode

OK, I will develope such a program myself!

ADD REPLY • link 12.3 years ago by Free Man ▴ 180

score 5 · Answer 1 · 2011-12-23

5

Entering edit mode

12.3 years ago

Chris Miller 22k

You might try snpEff or Ensemble's Variant Effect Predictor

ADD COMMENT • link 12.3 years ago by Chris Miller 22k

score 3 · Answer 2 · 2011-12-23

3

Entering edit mode

12.3 years ago

Swbarnes2 ★ 1.6k

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

ADD COMMENT • link 12.3 years ago by Swbarnes2 ★ 1.6k

score 2 · Answer 3 · 2011-12-23

2

Entering edit mode

12.3 years ago

Gjain 5.8k

how about UCSC genome browser.

ADD COMMENT • link 12.3 years ago by Gjain 5.8k

score 1 · Answer 4 · 2011-12-24

1

Entering edit mode

12.3 years ago

Yuyin110 ▴ 10

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

ADD COMMENT • link 12.3 years ago by Yuyin110 ▴ 10