Questions tagged [mutations]

Nucleotide base changes in the genome from its parental copy which for eukaryotes or bacteria is DNA

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Is there a way to customize what observations are plotted in ComplexHeatmap?

So right now my observations in the dataset I've processed is stored as sample identifier columns and gene rows: an example of this would be for sample 1 and gene TRIM21 the observation is Missense ...
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14 views

Residue coevoution from position wise residue preferences rather than multiple sequence alignments

Hello experts in residue coevolution analysis of proteins, I am looking for a way to calculate residue coevolution (coupling scores) between all pairs of residues of a protein. The issue is that ...
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1answer
43 views

How to calculate mutation rate and mutation sites in a genome using FASTA file?

I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format. I want to know, how I can identify mutations and mutation sites in those genomes using FASTA sequences (If I'...
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1answer
29 views

Model the effect of treatment on mutation burden

I am struggling a bit to model the following problem. Basically, I would like to model tumor mutation burden (mutations per megabase, a continuous) as a function of treatment (categorical). The ...
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1answer
32 views

Is there a tool for synonymous recoding of DNA sequences?

I've got a DNA sequence that I'd like to make synonymous mutations throughout, thereby preserving the amino acid sequence. Does anyone know of a tool to achieve this
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1answer
32 views

Is there a aminoacid mutation that forms similar protein? [closed]

Is there an amino-acid shift that will 99% of the time end up resulting the same biochemical function/structure and implications? Like Alanine replaced by Leucine will code in 99% of the cases(at any ...
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22 views

How to find the region with frequent mutation?

I am very new to bioinformatics and I was wondering if I can get some help regarding finding region that has high mutation rate. Currently, I have 2 fasta files, one that is aligned and one regular ...
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46 views

Finding difference between groups

I have mutational catalogues of 4 samples like below ...
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10 views

Scooping and GeneMatcher

A colleague has uploaded about a dozen candidate disease genes to GeneMatcher with excellent success. However last year and again recently he has encountered the case wherein a case was uploaded and a ...
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1answer
50 views

Are there databases to annotate non-coding mutations?

I would like to ask if there are some known databases that allows to annotate non-coding mutations in a given region for the human genome? Preferably, if the database is downloadable so I am able to ...
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27 views

Need help in identifying origin of variants in CIVIC

We usually denote the origin of a mutation as either somatic or germline. This information is usually available in certain databases such as CIVIC, ClinVar, COSMIC etc. But when we come to variants ...
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1answer
126 views

Plot a circos plot to show the consistency between 2 samples

I have called SNP and INDEL in two matched samples by strelka and extract this information from .vcf file and I have these ...
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100 views

maf file format: Variant_Classification value for non frameshift substitution

I have a vcf containing SNV and MNV (short indells or substitutions), I annotate that file whit annovar and in the resulting txt file I have this row ...
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3answers
81 views

Which gene I should select from this qqplot

I have a qqplot of my whole genome sequencing data; A plot is for showing possibly significant driver genes. I tried to read about qqplot though but people only say about the skewedness while I want ...
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39 views

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 ...
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0answers
131 views

Meaning of category in MutSigCV

I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is category. According to MutSigCV, every mutation can be divided into the following ...
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1answer
47 views

How can I get a list of papers where a particular mutation has been mentioned?

I have recently tried a few tools (MutationFinder, tmVar, PubTator etc.) that extract mutations from a given text. However, for my work I need something that will take a list of mutations as an input ...
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1answer
44 views

tool for the prediction of impact of mutations on protein localization

I need to know if the mutations present in the "position of interest" can have an impact on the protein localization ability. Is there any tool to make such prediction that can make my life easier? ...
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1answer
61 views

how to do analysis of a table content SNP?

I have a table with information about SNPs, the table has a total of 55127 rows. How can I know the number of gene mutations in the table and if a gene is present? The table is in xls format.
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1answer
150 views

How to get unique somatic mutations for each individual patients

I have exome data 32 patients. My aim is to identify unique somatic mutations in each patients. For this I have completed my pipeline for Whole Exome Data analysis using various tools like BWA mem, ...
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1answer
102 views

Information about control data

I am putting this question because I did not find any useful information from internet because of limited access. My question is related to control (or normal) data that we use for somatic mutation ...
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1answer
342 views

Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment

My task is to count the mutations occurred in several proteins after a treatment. The sequences are all present in the two files in the same order. I opened both files with the FASTA parser (...
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3answers
142 views

Show presence of known mutation in RNA-seq data

We have RNA-seq fastq data from control (WT) patients and a patient with a point mutation at a known location in one gene. I'd like to retrieve the reads aligning to that gene and show the presence of ...
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1answer
53 views

Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?

I have a set of whole genome sequencing samples, some of which have matched normal while some not. I want to call somatic mutations on non-coding regions. I was looking for GATK best practices (like ...
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1answer
341 views

State of the art mutation simulation software

There are many features affecting mutation probabilities, e.g. CpG mutations are 10-fold more likely than other types of mutations. Is there a model (preferably with software) which can take two ...