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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How can we map cis-regulatory elements to their specific promoter regions?

I'm trying to map cis-elements to the promoter regions of the genes of interest we have. I don't have a database I'm working from, but I have a list from the new-place, sogo website; outputs format into Factor site, Loc, Str, SITE So I have the…
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How do you loop and match column 1 and 2 of file1 with cell in column1 of file2 in order to replace them with the adjacent cell in column 2 of file 2?

I am using String-db interactions for a project but I found out that the complete list of interactions uses their ensembl protein IDs. I would like to replace those ensembl protein ID names with their HGNC approved gene symbols. Using BioMart, I…
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find minimum of math function with genetic algorithm in matlab, I know matlab have toolbox for GA but I want achieve it programmatically

find minimum of math function with genetic algorithm in matlab What modification are needed in this files-main.m? global population; global fitness; global popsize; format…
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Mutation step/symbol size when plotting haplotype networks with pegas

I've been trying to figure out how to make the little circles that represent mutation steps on a haplotype network bigger. For whatever reason, all the normal ways I'd think don't seem to be working. It seems like no matter what I do, the symbols…
Luther Blissett
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Rearrange strings in list alphabetically and by case

I have a list in a for loop and it uses itertools.product() to find different combinations of letters. I want to use collections.Counter() to count the number of occurrences of an item, however, right now it prints all the different combinations of…
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Error in champ.lasso of ChAMP Bioconductor package for Methylation 450k analysis

I have just installed ChAMP and all of its dependencies for methylation 450k analysis. I was trying out the tutorial (http://www.bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.pdf) but got an error. When running the Probe…
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Is there an R function that can find (like count) and give position of string?

I am looking for code in Rstudio that will search for Recombination signal sequences (RSS) within a DNA sequence and give me the position. I used count function however it does not give me position and I cannot input multiple RSSs into it at the…
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Get Gene IDs for a list of Gene Names in R

I have a huge list of gene names, and I'd like to map corresponding gene IDs to each name. I've tried using this R library: org.Hs.eg.db, but it creates more IDs than names, making it hard to map the results together, especially if the list is…
Bayram Sarilmaz
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snp to gene mapping with lowest p value

I am doing snp to gene mapping and after mapping with 50 kb of snp, I have following file. for example (snp,gene,pvalue) 1. ars113 ap1 0.1 2. ars113 ap1 0.1 3. ars113 ap1 0.2 4. ars113 ap1 0.2 5. ars113 ap2 0.1 6. ars113 ap2 0.2 7.…
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Replace tip of newick file using reference list in bash

I have a collection of newick-formatted files containing gene IDs: ((gene1:1,gene2:1)100:1,gene3:1)100; ((gene4:1,gene5:1)100:1,gene6:1)100; I have a list of equivalence between gene ID and species name:…
tlorin
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How to run PCA, distance matrix and other math procedures on genome VCF files in R?

I am learning to process VCF (variant call files) to produce plots and reports. Here is the R code, which crashes for unknown to me reasons. Please advise how to fix it and tell appropriate tutorials. library(VariantAnnotation) …
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How to combine txt file to convert in Plink format

My 26 data files (.txt) (imputed genotypes for each chromosome) look like: CHR SNP1 SNP2 SNP3 1 3 1 2 3 1 3 0 2 1 1 0 0 1 0 1 0 3 3 1 1 1 1 0 2 CHR SNP1 SNP2 SNP3 2 1 1 2 2 2 0 3 1 1 2 0 …
user2808642
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