Questions tagged [mutations]
Nucleotide base changes in the genome from its parental copy which for eukaryotes or bacteria is DNA
34
questions
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0answers
25 views
Alignment with inserts and keeping the indexing of ref seq intact
Parts of sequences are given below-
Reference sequence (pre-alignment):
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGT
...
2
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1answer
29 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 ...
1
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1answer
22 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.
...
0
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0answers
21 views
Detection of biallelic mutation (inactivation)
By biallelic mutation (inactivation), I mean several cases:
The first mutation is inherited (germline) mutation and the second mutation occurs as somatic at other loci, but within the same gene. Each ...
2
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1answer
26 views
Python package or CLI tool outputting mutations of sequence with respect to reference
I'm new to bioinformatics, and I'm looking for a tool that takes two FASTA files, one containing a reference, let's call it A.fasta, the other another sequence, let'...
1
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1answer
99 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 ...
1
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1answer
34 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, ...
0
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0answers
6 views
Mutated residue number shown wrong in foldX yasara
I am trying to mutate phenylalanine 274 position in Uracil DNA glycosylase with alanine. The pDB file has the protein starting from 82nd residue. After the repair the console shows FA161A. The residue ...
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0answers
41 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 ...
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0answers
11 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 ...
0
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1answer
37 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 ...
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0answers
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 ...
0
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1answer
129 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 ...
1
vote
1answer
46 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 ...
1
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2answers
69 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
0
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1answer
35 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
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1answer
57 views
1
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1answer
21 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 ...
1
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1answer
59 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
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0answers
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
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1answer
190 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
...
0
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0answers
148 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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3
votes
3answers
96 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 ...
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0answers
41 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
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0answers
141 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 ...
3
votes
1answer
48 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
1answer
65 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.
2
votes
1answer
193 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, ...
0
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1answer
104 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 ...
1
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1answer
447 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 (...
5
votes
3answers
193 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 ...
1
vote
1answer
57 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 ...
11
votes
1answer
357 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 ...
