Duplication Mutation prediction
1
0
Entering edit mode
4.5 years ago
yoosefyud ▴ 40

Hello everyone... I need to predict a duplication mutation error with mutation taster. what i understand from mutation taster help , it can't predict duplication mutations like c.1312dupC . Is there a way to use that for duplication mutations? If not, please introduce me proper database. also please help how can i insert intronic mutation like c.1682-1G>C in that database. Thanks a lot.

genome snp • 1.5k views
ADD COMMENT
2
Entering edit mode
4.5 years ago

Almost all in silico pathogenicity / functional impact prediction algorithms that have been developed have been developed for single nucleotide variants, whether coding or non-coding. However, algorithms that claim to be able to predict the impact of indels (your duplication event can be regarded as an insertion of C) have been appearing relatively recently, including:

I'm linking you to the published manuscript relating to each tool, here. There are web-based implementations of these too.

In order to use these, you will most likely have to convert your HGVS format to something like, for example, chr start end ref alt. This program, implemented in Python, can apparently do just that: https://github.com/biocommons/hgvs

Kevin

ADD COMMENT
0
Entering edit mode

I am so grateful for your help Mr glighe.

ADD REPLY

Login before adding your answer.

Traffic: 2672 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6