How To Study Effects Of Mutations

Question

[Huma]

Hi, Can anyone kindly tell me about the steps to study the effects of single base mutation in a DNA sequence?

[Chris Evelo]

Since you added the protein tag I suppose your question is really about a mutation that affects the coding sequence?

[Larry_Parnell]

Is this a human sequence? If not, which organism?

Answer 1

[User 59]

Have a search on this site for SIFT and PolyPhen - these all predict effects of DNA mutations on protein function:

Here's your starter for 10

There's also SNPtoGO, and many other tools. 'Missense' is another good search term for this site.

Answer 2

[Bert Overduin]

Hi,

There is also the Variant Effect Predictor of Ensembl, which is offered as a web interface (for small numbers of variants) as well as a Perl API script:

http://www.ensembl.org/tools.html

Answer 3

[Sophia]

Try also Condel , which combines several of the above mentioned methods variant effect prediction methods.

[Liyf]

By the way, I used Condel, but found that different transcripts in the same gene, it would predict different results, how can I combine them?

[Sophia]

@liyf: That would depend on the aim of your study. A given variant may have a different impact on different transcripts of the same gene. Each line of the Condel output gives you one variant in one transcript with one prediction of deleteriousness. You could e.g. select transcripts that are likely to be expressed in your sample and look only at the prediction for those transcripts.

Answer 4

[Pablo]

http://snpeff.sourceforge.net/

Answer 5

[Tim]

Since you've added the protein tag I thought I'd link this:
http://www.cmbi.ru.nl/hope/home

It studies the structural & functional effects of a single protein point mutation fully automatically and displays a readable report with illustrations, which could be a nice start off point for further analysis. See also: "*Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces*"