Question: How To Study Effects Of Mutations
3
gravatar for Huma
9.3 years ago by
Huma30
Huma30 wrote:

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

protein mutation • 3.5k views
ADD COMMENTlink modified 9.3 years ago by Sophia300 • written 9.3 years ago by Huma30
2

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

ADD REPLYlink written 9.3 years ago by Chris Evelo10k
1

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

ADD REPLYlink written 9.3 years ago by Larry_Parnell16k
3
gravatar for Daniel Swan
9.3 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

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.

ADD COMMENTlink modified 10 months ago by RamRS27k • written 9.3 years ago by Daniel Swan13k
2
gravatar for Bert Overduin
9.3 years ago by
Bert Overduin3.7k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.7k wrote:

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

ADD COMMENTlink written 9.3 years ago by Bert Overduin3.7k
2
gravatar for Sophia
8.9 years ago by
Sophia300
Barcelona
Sophia300 wrote:

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

ADD COMMENTlink written 8.9 years ago by Sophia300

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?

ADD REPLYlink written 8.4 years ago by Liyf290

@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.

ADD REPLYlink written 8.4 years ago by Sophia300
1
gravatar for Pablo
9.3 years ago by
Pablo1.9k
Canada
Pablo1.9k wrote:

http://snpeff.sourceforge.net/

ADD COMMENTlink written 9.3 years ago by Pablo1.9k
1
gravatar for Tim
9.3 years ago by
Tim320
Nijmegen, the Netherlands
Tim320 wrote:

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*"

ADD COMMENTlink written 9.3 years ago by Tim320
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 998 users visited in the last hour