Questions tagged [mutations]
Nucleotide base changes in the genome from its parental copy which for eukaryotes or bacteria is DNA
44
questions
4
votes
1
answer
43
views
Identifying somatic mutations in cell lines
I would like to identify the somatic mutations present in a cell line and characterise the genes that are potentially affected by those mutations. For example, are there oncogenes mutated in a ...
- 160
4
votes
1
answer
67
views
calculating mutation frequencies for every gene
I have a dataset for mutation data and I want to calculate mutation frequencies across all genes
df (This is only the small subset of data)
...
- 351
-1
votes
2
answers
42
views
To find amino acid substitution from fasta alignment
I have fasta multiple sequence alignment file of protein sequence. I want to look for mutation/substitution in amino acid between query with reference to one query. Is there any R package or any ...
0
votes
0
answers
12
views
Differences between positionscan and buildmodel in foldx5?
They both output ddg and pdb file, but the positionscan command's ddg value is fixed, the buildmodel command's ddg value can be changed?
2
votes
1
answer
61
views
Sanger sequencing annotation error
I am a student in a Cancer lab. Working with sanger is new to me. While analyzing a report we found an insertion that has not been reported in any databases so far, we were working on checking if the ...
- 21
1
vote
1
answer
51
views
How to identify mutations in a viral genome
I have a fasta file with multiple sequences comprising 38 sequences. The length of the sequences are around 11000 bp.
How can i get changes in the genomes based in a reference genome? (aa subtitutions ...
2
votes
1
answer
204
views
How to calculate average BLOSUM62 scores?
I can understand the motive behind the BLOSUM62 matrix, this being a pairwise mutation matrix describing aggregate mutations between the 20 amino acids.
However how would you calculate the average ...
5
votes
3
answers
747
views
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 ...
- 151
3
votes
0
answers
45
views
How to use hgvs to project a variant list on a given protein sequence string?
I have the following protein structural variance list:
...
- 1,417
2
votes
3
answers
87
views
Can we do NGS library preparation using UMI with large amount of DNA input?
We know that in next-generation sequencing (NGS), the unique molecular identifier (UMI) can reduce or eliminate sequencing or PCR errors and result in very high accurate data. Therefore, UMI is widely ...
- 21
2
votes
1
answer
117
views
Caching and parallelization
Currently algorithmically developing a calculation for "co-dependent" mutation (quotation appropriate). The algorithm uses chunked biopython alignment objects which are parallelized.
Aim
One ...
M__♦
- 10.4k
1
vote
1
answer
177
views
VCF or BAM file for raw data of gene test?
My friend has a VUS (Polymicrogyria with or without VEDS) mutation that was found in her whole-exome sequencing with respect to the phenotype given that time. At present, her doctors have more ...
-1
votes
2
answers
198
views
Error in running Mutect2
I am trying to run Mutect2 on a .bam file but I get an error by Googling can not be tackled
Have you seen this error?
...
- 1,801
2
votes
0
answers
31
views
Alignment with inserts and keeping the indexing of ref seq intact
Parts of sequences are given below-
Reference sequence (pre-alignment):
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGT
...
- 145
2
votes
1
answer
44
views
Counting the co-occurrence of variants A and B in an aligned sequencing read
I need some help getting started on this project.
To simplify we want to be able to quantify the occurrence of 3 variants on each sequencing read in an alignment file as a proxy measurement for ...
- 21
1
vote
1
answer
29
views
A unified database for CNV, SNP, Indel and MSI
I am looking for a database or different databases where I can find information on different gene variants for a gene. As an example if I enter PPARG, I could be able to see SNPs, CNV, InDels and MSI.
...
- 175
1
vote
1
answer
292
views
How do I create a VCF file of all known pathogenic mutations in a gene of interest?
I would like to create a list (probably .vcf format would be good) of all known pathogenic missense mutations in a human gene of interest and then add other variants that could lead to the same ...
- 11
1
vote
1
answer
105
views
How to calculate various properties of a protein structure per atom using PDB2PQR and Rosetta tools (or any other tools)?
Currently, I am implementing a descriptor of protein structure and would like to calculate properties per atoms like charges, hydrophobicity, hydrogen bond donors / acceptors, hydrophobicity, ...
1
vote
1
answer
77
views
1
vote
0
answers
46
views
Somatic mutations for normal WES samples
I am trying to identify somatic mutations on healthy subjects (specifically in WES samples). As of now, I have found a couple of papers who have done similar studies such as this paper where somatic ...
- 560
1
vote
0
answers
15
views
How do I include repeat purity, default slippage, default stutter, and minimum flanking (left and right) in Tandem Repeat Finder's output?
I am attempting to create a markerInfoFile for use in a program called popSTR (GitHub Documentation: https://github.com/DecodeGenetics/popSTR). The marker info file should contain information about ...
- 169
0
votes
1
answer
88
views
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 ...
1
vote
0
answers
17
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 ...
- 665
0
votes
1
answer
279
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.
How I can identify mutations and mutation sites in those genomes using FASTA sequences but how I can do ...
- 75
1
vote
1
answer
69
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 ...
- 21
1
vote
2
answers
101
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
- 113
0
votes
1
answer
48
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 ...
0
votes
1
answer
76
views
1
vote
1
answer
23
views
Scooping and GeneMatcher
A colleague has uploaded about a dozen candidate disease genes to GeneMatcher, described here and here and located here, with excellent success. However last year and again recently he has ...
- 4,124
1
vote
1
answer
83
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 ...
- 1,055
1
vote
0
answers
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 ...
0
votes
1
answer
270
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
...
- 1,801
1
vote
0
answers
227
views
maf file format: Variant_Classification value for non frameshift substitution
I have a vcf containing SNV and MNV (short indells or substitutions), I have annotated that file with annovar and in the resulting txt file I have this row:
...
- 323
3
votes
3
answers
110
views
Which gene I should select from this qqplot [closed]
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 ...
- 1,801
1
vote
0
answers
56
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 ...
- 1,773
2
votes
0
answers
151
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 ...
- 560
3
votes
1
answer
49
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 ...
2
votes
1
answer
100
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.
- 351
2
votes
1
answer
230
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, ...
- 560
0
votes
1
answer
105
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 ...
- 560
1
vote
1
answer
587
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 (...
- 21
6
votes
3
answers
212
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 ...
- 2,604
1
vote
1
answer
60
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 ...
- 1,773
11
votes
1
answer
366
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 ...
- 2,715