Questions tagged [genetics]

The scientific study of the principles of heredity and the variation of inherited traits among related organisms.

Genetics is the study of genes — what they are, what they do, and how they work. Genes inside the nucleus of a cell are strung together in such a way that the sequence carries information: that information determines how living organisms inherit various features (phenotypic traits). For example, offspring produced by sexual reproduction usually look similar to each of their parents because they have inherited some of each of their parents' genes. Genetics identifies which features are inherited, and explains how these features pass from generation to generation. In addition to inheritance, genetics studies how genes are turned on and off to control what substances are made in a cell-gene expression.

Nowadays, the genetics is interesting in computer science too. It can propose own advances and results of the investigations to describe the information interpretation for very complex objects and needed methods on the algorithmic level. For example, one gene can save value about one feature of the object, furthermore, using different methods of information coding we can expand properties of one gene whereby different shades. Also, considering gene on the abstract level of our understanding, we can build a very powerful system of equations which will be describing the object completely from different aspects.

To know more.

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What is an idiomatic way of representing enums in Go?

I'm trying to represent a simplified chromosome, which consists of N bases, each of which can only be one of {A, C, T, G}. I'd like to formalize the constraints with an enum, but I'm wondering what the most idiomatic way of emulating an enum is in…
carbocation
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How much storage would be required to store a human genome?

I'm looking for the amount of storage in bytes (MB, GB, TB, etc.) required to store a single human genome. I read a few articles on Wikipedia about DNA, chromosomes, base pairs, genes, and have some rough guess, but before disclosing anything I'd…
Milan Babuškov
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How to plot positions along a chromosome graphic

I would like to generate a plot depicting 14 linear chromosomes for the organism I work on, to scale, with coloured bars at specified locations along each chromosome. Ideally I'd like to use R as this is the only programming language I have…
Will Hamilton
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How to create a Manhattan plot with matplotlib in python?

Unfortunately, I have not found a solution myself. How do I create a Manhattan plot within python using, e.g., matplotlib / pandas. The problem is that in these plots the x-axis is discrete. from pandas import DataFrame from scipy.stats import…
Thomas Möbius
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Map SNP IDs to genome coordinates

I have several SNP IDs (i.e., rs16828074, rs17232800, etc...), I want to their coordinates in a Hg19 genome from UCSC genome website. I would prefer using R to accomplish this goal. How to do that?
user1938809
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Complement a DNA sequence

Suppose I have a DNA sequence. I want to get the complement of it. I used the following code but I am not getting it. What am I doing wrong…
Anurag Mishra
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How to read vcf file in R

I have this VCF format file, I want to read this file in R. However, this file contains some redundant lines which I want to skip. I want to get something like in the result where the row starts with the line matching #CHROM. This is what I have…
MAPK
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Transposing a data frame

I am trying to transpose a data frame in R, but having very little luck. The data frame contains an epigenetic data set, with 300,000+ CpG sites in the first column. The 74 additional columns are split between the control and experimental groups…
statsguyz
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Genetic Engineering simulation

Does anybody have any good source of software/tutorial about Genetic Engineering Simulation? Maybe open source software about gene splicing / cloning simulation ? Thanks
Lydon Ch
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How to combine all chromosomes in a single file

I downloaded 1000 genomes data (chromosome 1 -22), which is in VCF format. How I can combine all chromosomes in a single files? Should I first convert all chromosomes into plink binary files and then do the --bmerge mmerge-list? Or is there any…
bha
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How to compute p-values from z-scores in R when the Z score is large (pvalue much below zero)?

In genetics very small p-values are common (for example 10^-400), and I am looking for a way to get very small p-values (two-tailed) when the z-score is large in R, for example: z=40 pvalue = 2*pnorm(abs(z), lower.tail = F) This gives me a zero…
user971102
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Generating Random Variables with given correlations between pairs of them:

I want to generate 2 continuous random variables Q1, Q2 (quantitative traits, each are normal) and 2 binary random variables Z1, Z2 (binary traits) with given pairwise correlations between all possible pairs of them. Say (Q1,Q2):0.23 (Q1,Z1):0.55…
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Filter Dictionary According to Existing List

Still a Python novice so please go easy on me... I've got a dictionary set up: new_dict I'd like to filter to return the keys, where any of the values attached to each key match the value in an existing list I have set…
cps1
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A way of testing a set of genomic locations for exon/intron/utr?

I would like to test a bunch of genomic locations of the form: chr4:154723876-154724615 chr6:139580853-139581090 chr18:30440532-30441569 I want to see whether they are located in an UTR or intron or exon or an intergenic sequence. I don't care for…
yotiao
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How to edit 300 GB text file (genomics data)?

I have a 300 GB text file that contains genomics data with over 250k records. There are some records with bad data and our genomics program 'Popoolution' allows us to comment out the "bad" records with an asterisk. Our problem is that we cannot find…
Keith W. Larson
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