Questions tagged [point-mutation]

Single mutation in the DNA or RNA for RNA viruses, also known as single nucleotide polymorphism (SNPs)

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How to associate point mutations to quantitative protein levels

My experiment is based on a quantitative continuous variable levels (B12 vitamin) in a sample of patients retrospectively selected based on values that can take (under our criteria): normal low ...
Javier Hernando's user avatar
2 votes
1 answer
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calculate mismatch frequency/rate from a BAM file

I am working with PAR-CLIP data where experimental procedure induces T to C mismatches. The other types of mismatches we can consider coming from artifact such as PCR errors. It could also be an ...
Ahsan's user avatar
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Why can't AlphaFold predict the consequences of point-mutations?

In the literature, it specifically states that AlphaFold has "Has not been trained to predict structural consequences of point mutations". See : https://alphafold.com/faq AlphaFold has not ...
jambajuice's user avatar
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What are values of FILTER column of vcf files produced by Mutect2

I have called SNVs with Mutect2, now in filter column of a file called filtered vcf I have a lot of things like ...
Zizogolu's user avatar
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Are there different PAM matrices for different protein families? - How is the inferred common ancestor known to start with?

I am confused about the sequences one starts with to generate the PAM matrices. The sequences to start with are supposed to diverge by no more than 1% (in sequence identity) wrt a common "...
Gordon J. Köhn's user avatar
1 vote
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Site Mutations in a 3D protein structure to locate the core of mutations

I have a pdb file for a protein (3D structure predicted by a tool) and around hundreds of known point mutations in the protein. I want to visualize the protein with all the mutations to see the hub of ...
saamar rajput's user avatar
3 votes
1 answer
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How to introduce point mutations in a protein structure?

I want to introduce point mutations to a protein PDB file and automatically predict the 3D coordinates of a new amino acid residue in the mutated protein. I used interactive Schrodinger's Maestro tool ...
Nurlybek Amangeldiuly's user avatar
1 vote
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How to select point mutations from MAF file

I am using a mutation MAF file from GDC. I want to select for point mutations, therefore I selected Variant_Classification equal to ...
gc5's user avatar
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