All Questions
Tagged with genetics bioinformatics
109 questions
0
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43
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Can We Determine the Cell Types Ab initio?
Is it possible to find all cell types in the human body and their respective transcriptomes by analyzing the human genome (and doing no physical experiment)?
If such a thing is possible in principle, ...
0
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0
answers
36
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How do genetic variants of a gene moderate an association, leading to counterintuitive result?
I have run moderation analysis to study the interaction between SNP (dominant model) of a gene (A) with DNA methylation on cognition measures. For this, I have calculated the mean DNA methylation ...
- 29
7
votes
1
answer
120
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How can I find/simulate mixed-ancestry DNA data?
Some collaborators and I are building an ancestral inference tool, and we're having trouble obtaining reliable ground-truth data for samples of mixed ancestry. All the ground-truth DNA datasets we're ...
- 73
2
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1
answer
65
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Making sense of infinite-sites mutation but finite-sites recombination coalescent simulator
Hudson (1983) introduced a coalescent simulator with infinite-sites mutations and finite-sites recombination. This seems paradoxical because the documentation of the simulator (section on crossing ...
- 123
2
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0
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87
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Difference between heritability on the scale of liability versus the scale of observation
I was reading a paper on disease heritability ("Estimating Missing Heritability for Disease from Genome-wide Association Studies") and it struck me that I don't have a great understanding of ...
- 21
1
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1
answer
56
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Does gene isoform have different genetic location?
I would like to understand how a gene is assigned to a specific coordinate (e.g. NOC2L Chr1 879583(Start) 894679(End)). Next, let's say NOC2L gene has a few different isoforms, do those isoforms ...
0
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1
answer
111
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Get "DNA" of one parent based on its children [closed]
I'm no biology expert so bear with me, but I've been given a task to estimate alleles of an animal based on the animal's children and the children's other parents.
I've looked up Mendel's laws but I'm ...
- 111
0
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1
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409
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How to identify an unknown species from its genome sequence [closed]
I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to ...
- 186
3
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1
answer
93
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Rigorous definition of the kinship coefficient and proof of a recursion thereof
I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...
- 486
1
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1
answer
94
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Help Finding Specific BlaZ Gene Type Sequences on Genbank
I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that ...
1
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1
answer
76
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BLAST, using Smith-Waterman in the last step and S-score
In my bioinformatics course we studied the BLAST agorithm. After finding the HSP's and joining the HSPs together that are close enough and in a correct diagonal trend, we perform a next step: namely a ...
1
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1
answer
33
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Why the major gene model can be supported by finding de novo mutations in affected cases?
I found a sentence which I can't fully understand in a publication on the genetics of autism.
The unified major gene model is supported by the significant increase
in damaging de novo mutations ...
- 13
1
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1
answer
65
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How accurate are Illumina microarray chips for genotyping?
What is the error rate for these machines in genotyping (like for 23&me)? What is the chance of a false positive or false negative?
- 399
0
votes
1
answer
85
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How to search for a DNA sequence in a genome on ENA (European Nucleotide Archive)?
I have to do a search for small DNA sequences in the genome of an organism in ENA. I have the accession number and project id. However, I can't download the whole genome because of the download size ...
0
votes
1
answer
63
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What are primary reasons for the failure to localise/anchor sequences in genome assemblies?
My question concerns the incorporation of individual sequence reads into chromosomes during gene sequencing projects, especially those with larger genomes such as Drosophila melanogaster or Homo ...
- 53
1
vote
1
answer
157
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How to download different kinds of data from NCBI eutils?
I have been researching NCBI eutils and wish to get some 'big data' from it. I know that I can construct queries to query one of (I think) 8 databases, like this:
...
- 143
1
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2
answers
476
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GEN file format, SNPs and alleles
I have a few questions I can't seem to get a straight answer to, regarding the .gen file format and also biology in general.
The ...
- 123
1
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0
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60
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Projects in DNA Computing [closed]
I am physicist and have recently heard about DNA computing. I want to work in this area.
I want your ideas on a "feasible but new project" (maximum time I can put on the project: 6 Months ), I can ...
- 11
0
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1
answer
113
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Question regarding when it's a homoplasy in a phylogenetic tree
If you have 2 organisms that both come directly from the same common ancestor on a phylogenetic tree, and that common ancestor does not have trait "x", is it possible for both of its direct ...
2
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2
answers
350
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Meaning of Phred score - probability of base calling error
I learned that Phred quality scores are logarithmically linked to error probabilities. For example, if Phred assigns a quality score of 10 to a base, the chances that this base is called incorrectly ...
- 41
2
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3
answers
312
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Strand representation in the DNA version of the Genetic Code
A Wikipedia entry entitled DNA Codon Table states that the codons presented in the table are on the ‘sense strand of the DNA’. But what is the purpose of this, if the sense strand doesn’t code for ...
- 327
0
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3
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254
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why and how multi allele gets reported during variant calling in vcf?
This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can ...
- 101
1
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0
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19
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Is there any data to explore the heterozygosity of the South African lion over the last 18 years?
Background:
I need to find data on the heterozygosity of the south African lion over the last 18 years... and I'm struggling: so far I have found a single data point.
Question:
Where can I find ...
- 3,597
-2
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1
answer
64
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Genetic modifications in humans to prevent disease [closed]
I was reading an article about "designer babies", which was about how before birth the DNA can be modified so to achieve certain features. Can a technique such as this also be used to prevent diseases,...
- 101
0
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3
answers
77
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Is there any way to tell if a gene is functional for an individual with only a reference sequence and the individual's sequence of the gene?
I have gene sequence of a ton of individuals within a subspecies from cdna and the ncbi IDed sequence as well. Is there any way to tell using just the sequence that the gene for an individual is non-...
1
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0
answers
40
views
How does one calculate Rx/a in population genetics?
The ratio of sex-linked to autosome mutation frequencies (R) is Rx/a =(2/3)(2+ α)/(1+ α) for X-linked genes and Ry/a = 2 α /(1+ α) for Y-linked genes. How does one calculate Rx/a, in order to find α?
- 11
3
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0
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52
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How much Open Access Data is there in genetics? [closed]
Type of data of interest
I would like to consider
Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...)
Genetic - phenotype data (disease-related data, QTL, etc...)
Sequence ...
- 68.3k
2
votes
2
answers
304
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Which information can be extracted from time course RNA-Seq Data?
So I am very new to the area of biology so I am sorry if this is a stupid question.
I have RNA-Seq data carried out over a span of 100 days and I have gene expression data in the following format. ...
- 31
5
votes
1
answer
277
views
How much variation in mutation rate in there in the human genome?
In humans, the average mutation rate is estimated to be around $2.5 \cdot 10^{-8}$ (Nachman and Crowell, 2000). Of course this mutation varies from sequence to sequence.
Can you please give some ...
- 68.3k
2
votes
1
answer
115
views
Phasing haplotypes
I'm new to this area (but not to programming & algorithmics) and I want to help a friend to solve a problem (I don't need source code, I just want to understand the problem itself).
He needs a ...
- 235
0
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2
answers
90
views
Why would there be a spike in coverage within a gene in RNA seq data? [closed]
I'm looking at RNA seq data in Geneious for Salmonella typhimurium and I occasionally see a spike in coverage for a sequence of RNA within a gene. Why is there a section of the gene that seems to be ...
- 1
0
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1
answer
357
views
Inheritance of mitochondria [closed]
Imagine an isolated population in which each adult female has a distinct mitochondrial genome. In each generation, every adult female has two children (with a 50% chance of being male or female). ...
-2
votes
1
answer
286
views
Longest transcripts without isoforms
Does anyone know what genes produce the longest mRNAs? I am planning a project on synthetic introns and want to use stuffer fragments to vary intron size. Obviously they must not contain any splicing ...
- 7
3
votes
1
answer
113
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Webtool to design guide RNA (gRNA) for use with CRISPR-AsCpf1?
My goals are to use a free webtool to:
Identify guide RNAs (direct-repeat sequence followed by the targeting sequence) appropriate for use with AsCpf1 in order to target a specific segment of genomic ...
- 131
1
vote
0
answers
966
views
Understanding PAM and BLOSUM matrices
This question might be silly but I need some clarification.
I'm slightly confused about if there are multiple PAM and BLOSUM matrices? Is there a different matrix for each sequence?
My ...
- 143
3
votes
1
answer
511
views
What is meant by “genes at the trunk of the evolutionary tree”?
Recently I went through a paper about hepatocellular carcinoma in which they talked about trunk genes (p. 26, second paragraph):
Branching tumor evolution complicates efforts to implement
...
- 209
2
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1
answer
58
views
How can I list genes present on a given series of bands?
My question is related to this one. My interest relate to this deletion:
del(7)(q11q36)[12]
as defined by ISCN.
I would like to access a list of the genes found on the bands 11 to 36 of the 7th ...
- 68.3k
2
votes
2
answers
313
views
Actual determination of the DNA sequence in the shotgun approach?
I'm studying bioinformatics and I'm confused by shotgun sequencing. In Sanger sequencing we break up the DNA and use ddNTPs in order to determine the exact position of each neucleotide. How exactly ...
- 143
1
vote
1
answer
87
views
What is Genome wide analysis and Locus specific analysis
I am reading some articles on genetic variations and I see there are two types of analysis one is genome wide genetic variation analysis and second one is locus specific genetic variation analysis. I ...
- 187
10
votes
1
answer
6k
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Why should we use the NA12878 dataset for benchmarking?
As far as I understand, the human genome sample called NA12878 provides high confidence variants for a human sample. It is being used as a benchmark for many genomic research projects.
Q: Why exactly ...
- 1,029
1
vote
1
answer
395
views
Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?
I have a data set of de novo assembled RNA-seq datasets across different sample types.
When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. ...
- 101
4
votes
0
answers
667
views
Minor Allele Frequency (MAF) higher than 0.5? [closed]
I have a set of data in PLINK format (*.bed, *.bim and *.fam files). There are around 2000 individuals in my dataset.
I used PLINK to calculate allele frequencies in the population:
...
- 41
11
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2
answers
1k
views
Books on machine learning applications in Biology
I have recently engaged with a collaboration, which requires me to construct, then train an unsupervised artificial neural network (ANN).
However, I have only a very coarse understanding of what ...
- 3,597
0
votes
1
answer
628
views
How to find the location of a gene, starting with the gene name and the DNA sequence of nucleotides? [closed]
I'm not a professional biologist, I'm just trying to analyze some actual data. Where should I look up the location of a gene and nucleotides it consist of? How can I find it in DNA? Is there an ...
- 103
5
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1
answer
445
views
How valid are GO (Gene Ontology) terms?
I'm looking for papers quantifying the validity of ontologies such as GO.
I'm relatively new to using annotation terms, and I often hear things like "annotation is messy" and "GO is good but it's ...
- 247
12
votes
1
answer
475
views
Which is the reference 16S rRNA?
Recently, I've stumbled upon a fact, which hasn't bothered me for many years. The fact is that all universal 16S primers are written as "[FR][0-9]+" (in regex notation), that is they have a position ...
- 1,007
2
votes
1
answer
546
views
How to get the average number of pairwise differences among populations?
I have genetic data in .structure and .vcf format (and can easily reach other formats with PGDSpider). The population of interest is structured and I would like to calculate the average number of ...
- 68.3k
2
votes
0
answers
63
views
Finding diploid neanderthal alignment data, looking for ambiguity codes
I'm using Neanderthal alignment data from here: http://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html
Specifically, the .bam files. I would like to find alignments for neanderthal ...
- 75
1
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0
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34
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Quantifying the number of fragments from RAD library
I have a series of single-end reads from a RAD library of 48 uniquely tagged individuals in fastaq format. The data comes from a small MiSeq run. I want to know the number of unique fragments per ...
- 121
1
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0
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30
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Is there a place or tool from which I can find or generate genome data for epistasis detection?
I am busy researching a school project for my honors in Electrical Engineering. The project is to create a deep neural network to detect epistasis. I have very little knowledge in the bioinformatics ...
- 111