All Questions
Tagged with inheritance or genetics
371 questions with no upvoted or accepted answers
2
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How I can find the list of transcription factor proteins involved in transcription of a specific gene?
I want to get the list of transcription factor proteins involved in the transcription of the human SIRT1 gene. How can I access that?
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2
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0
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64
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What is the DNA sequences between two Inverted Repeats called?
I would like to know some rules about the nomenclature of Inverted Repeats DNA sequences. More in detail, I want to know what is the name of sequences between two inverted repeats.
For example, I have ...
- 21
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 ...
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2
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43
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Can chain-linked genetic segment data be used to reliably assign unknown relatives to either the donor's mother or father?
I am analyzing DNA matching segment data, and I am trying to broadly group all DNA matches by my donor's parents.
Based on documented evidence, I can confidently identify "Person 'B'" as a ...
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2
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238
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What does it mean for a protein to be dominant-negative?
I am reading this journal paper, which investigates the interaction of the NCAM protein and the Pak1 protein. In this paper I have come across the term "dominant-negative Pak1" and "...
- 1,761
2
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101
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What is the charge of (bacterial) ribosome?
Ribosomes are negatively charged and thus electrostaticaly repelled from DNA. However, I could not find a good reference that would allow me to estimate the magnitude of negative charge on a ribosome. ...
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2
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59
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What the "due to" means in the definition of heritability?
According to Wray and Visscher,
heritability is formally defined as the proportion of phenotypic variation (VP) that is due to variation in genetic values (VG).
My question is, what does “due to” ...
- 121
2
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122
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Recombination due to crossover, outcome?
Garden peas normally have 7 pairs of chromosomes (n=7, 2n=14). Please calculate how many different types of gametes can be produced through the meiotic process if no crossover happens. If cross-over ...
2
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24
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Need help to determine % difference between DNA-strand from two different haplotypes. Known nucleotide diversity and more
Backround:
229 DNA sequences
493 bp in length
Haplotype diversity: 0.9956
Average number of nucleotide differences: 12.50544
Polymorphic sites: 145
Nucleotide diversity: 0.02426
Is it possible ...
- 21
2
votes
0
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254
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what is the difference between homozygous and heterozygous duplication?
In a genetic test result it's written
homozygous duplication
or
heterozygous duplication
Does it mean four copies of the ...
- 121
2
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answers
312
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What are the different types of SNPs?
When I search for this online I get answers such as substitutions, deletions, insertions etc. But I mean in the sense that I have been reading different terms infront of the word SNP such as: lead SNP,...
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2
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68
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Which enzyme is Nick Lane referring to?
In Life Ascending the author, Nick Lane, refers to an enzyme in his introduction:
'' It concerns an enzyme (a protein that catalyses a chemical reaction) that is so central to life that it is found ...
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2
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answers
54
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Does the male and female always split evenly the genetic material given to their offspring?
Are there animals known to have a different percentage of splitting of genetic material, like the male give 75% and the female just 25%. I know that drone bees have only genetic material from their ...
2
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answers
217
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Honeybee relatedness: workers and nephews
This is my first question on this site. If anyone could help me get to the bottom of it, I would be very grateful.
I am currently working on a lecture on kinship in animals. It goes without saying, ...
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2
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58
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Could the Immune Gene HLA-B27 be gentically altered, snipped, switched off, replaced, edited within the body
Could the Immune Gene HLA-B27 be genetically altered, snipped, switched off, replaced, edited within the body.?
Thousands upon thousands suffer immune disease as do I from this highly implicated gene....
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2
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answers
30
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Estimating population divergence time with a single mitochondrial marker
Is it possible to estimate population divergence time with a single mitochondrial marker?
Here is additional information for my specific case:
Mitochondrial marker: Cytochrome Oxidase Subunit 1 (...
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2
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41
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why hens determine the sex of the chick?
So, I have an exercise where I have to correct the second part of the sentence. It goes like this:
In hens, the sex of the chicken is determined by hen, because the hen is the heterogametic ...
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2
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43
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Measuring gene similarity in two bacteria models
I'm currently working with some computational models of bacteria. The bacterium I am considering is an Ecoli K-12 which has 139 genes. I have several models of the same bacterium with different ...
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2
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0
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1k
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Can telegony happen in humans like in Telostylinus angusticollis?
Is it possible for a human male to transmit features of his phenotype via non-genetic semen-borne factors to his mate's subsequent offspring sired by another male? As it happens in flies (Crean et al.,...
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2
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0
answers
110
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Horizontal gene transfer and Botulinum toxin
Is it theoretically possible that any aerobic bacterium becomes able to produce Botulinum toxin as a result of horizontal gene transfer from Clostridium botulinum to that bacterium?
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2
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111
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How to determine if twins are identical or fraternal if only one is alive?
I had a twin brother who died at birth. I've missed him all my life, and have been curious to know if we were identical or fraternal.
Is there a test to determine whether we were identical or ...
user20124
2
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answers
39
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When to decide that two similar sequences are different genes or not?
Working on RNA-Seq data directed me to ask this question. In RNA-Seq jobs, after de novo assembly we have lots of transcripts with different rates of similarity (0 to almost 100 percent) that we ...
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2
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29
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Can a regulator genes be more highly expressed when it has more places to bind?
I am doing some research on small cell lung cancer and, from what I have found, many tumors show high levels of ASCL1, which is a regulator for neuroendocrine cell differentiation. However, no papers ...
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2
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0
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70
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Majority rule definition
In this book, they talk about the majority rule.
Majority rule, which retain s the edges present in more than 50% of the trees.
They used that rule also in ...
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2
votes
0
answers
491
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How would circular dominance of alleles be determined on the genetic level?
The distinction between dominant and recessive alleles seems to be due to loss or gain of function in the proteins they code for. Alleles have been observed exhibiting incomplete and hierarchical ...
- 201
2
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0
answers
53
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psbA-trnH intergeneteic spacer inversion
What kind of software tool would you recommend as best suited to detect psbA-trnH inverisons?
I have 1x coverage Sanger .fasta files and >2000 sequences, with 1 sequence per species.
Most tools I have ...
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2
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0
answers
67
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What is allele-specific binding?
So far all I have found is this:
https://www.biostars.org/p/132527/
My guess is that some alleles, for whatever reason, bind to things like transcription factors 'moreso' (for want of better word - ...
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2
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0
answers
44
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Validity of comparing gene expression levels between alive and <24h postmortem cohort
There is a recent paper about assessment of a suicidal risk in psychotic patients https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759104/
One of the important points is that the authors compare gene ...
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2
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39
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How do genes get passed from one hive to another?
In hive species, like honeybees, how do genes propagate from one hive to another?
If the queen only mates with drones from the same hive, and queens and drones are born to the hive they end up mating ...
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2
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2k
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What is the probability of an XX female or XY male?
Homework question
In genetics the chance of having a male or female is 50% for male and 50% for female. Using factorial method and Punnett Square prove or disprove the claim.
My answer
Using the ...
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2
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answers
63
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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 ...
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2
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0
answers
72
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Has a restriction enzyme ever been tagged?
As part of an experiment that I am preparing, it would seem necessary for me to tag a restriction enzyme (HaeIII to be exact) with GFP. I began researching its domains to determine whether to tag the ...
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2
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0
answers
48
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Breeding Southern Right Whales Genetics
I don't know much about biology. I just like watching David Attenborough videos and this made me curious.
I just watched this video about breeding Southern Right Whales, and these two quotes puzzled ...
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2
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answers
76
views
What is the best test for SNV clustering?
I am looking for a method to cluster single nucleotide polymorphisms based on clinicopathologic data (mainly receptor immunoistochemistry). So far, I've came up with only two that handle dummy ...
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2
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0
answers
151
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Amplified Fragment Length Polymorphism (AFLP) primers
I am trying to blast AFLP primer sequences to the genome to find the locations of the AFLP markers. However, I can't seem to find full alignments for the primers on the genome.
For example, in the ...
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2
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366
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RAD sequencing: choosing the appropriate enzyme?
I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
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2
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58
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How to identify genes in Ralstonia that synthesize PHB and promote granule formation?
The compound polyhydroxybutyrate (PHB) is of considerable industrial interest as a biodegradable substitute for plastic. PHB is synthesized from glycerol by the bacterium Ralstonia eutropha. PHB ...
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2
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321
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HIV and open reading frames
In Wilk et al. 2001 I saw that HIV has 3 open reading frames. In the Watts et al. 2009, I noticed they mentioned HIV has 9 open reading frames. I don't understand this very well.
e.g.
...
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2
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101
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Math backbone in biology/genetic
Are there any good books, that shows some advanced models in genetics particularly?
The problem is i don't see any good math model in genetics interactions exept combinatorics. I'd like to know what ...
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2
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0
answers
83
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Gel Electrophoresis
we add Etbr within the agarose gel but we do not add Etbr directly in native PAGE ?when we make agarose gel, we add Etbr before its solidification but we do not add Etbr when the native PAGE gel is in ...
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2
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0
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78
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Genotype-Phenotype databases?
Beyond the Stanford HIV database, what other databases out there provide a dataset linking virus/bacterial genotype to quantitative phenotype? I'm looking for high quality datasets to test machine ...
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2
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0
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83
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How does intron retention make the alternative transcript non-coding?
I faced with a non-coding transcript that specified as one the isoform of BIN1.
It sounds that this isoform generated as a result of alternative splicing with a intron retained; am I right? However, ...
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2
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0
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Why are published chromosome counts for polyploids often incorrect by an integer multiplication factor of the original diploid like count?
Why are published chromosome counts (done using techniques such as root smashes) for polyploidy flowering plants often incorrect by a multiplication factor of 2 or 3 from the original diploid like ...
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2
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0
answers
128
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Efficient algorithm to calculate various population divergence statistics
Intro and description of the data
I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format
...
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2
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0
answers
60
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Do The Traces Genetic Diseases Remain in families?
I know that there are certain diseases that are predominant on genes. But, is there any sort of surety that if parents are suffering from a disorder then their offspring has to suffer from the same. ...
2
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0
answers
80
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Why do restriction-modification systems work?
Some RM systems (restriction-modification systems) are plasmid-borne and are transferred through bacterial conjugation. As you all know, there are two genes in an RM system, the gene that codes for ...
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2
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0
answers
31
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Resource for finding Repressive/Inhibitory factors for a given gene?
I have a list of genes for each of which I'd like to find:
A list of transcription factors that up-regulate the gene
A list of inhibitory factors that down-regulate it.
I used this tool on Qiagen's ...
- 1,000
2
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0
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977
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Can sealed epiphyseal growth plates theoretically be restored via epigenetic or genetic methods?
I know that epiphyseal growth plates seal up once people become young adults and that it is currently impossible to restore them to actively produce new bone growth but, is it theoretically possible ...
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291
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How TCGA CNV values are calculated?
When I download CNV SNP array data for ovarian cancer from TCGA data portal, I see some very small numbers like -5, -6 in the "Segment_Mean" column of the segmentation data files. I am very new to ...
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2
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124
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Can two Hfr strains of E. coli conjugate?
Genetics textbooks (and some internet searching) yield abundant examples of Hfr strains conjugating with F- cells, but these sources are surprisingly silent regarding the results of an Hfr ...
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