Questions tagged [gene]

Use this tag to refer to the gene sequence/coding part of the sequence.

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1answer
21 views

Is there a Python program that is able to show convergent and divergent evolution on a phylogenetic tree?

I was wondering if there was a Python program that detects convergent and divergent evolution on a tree. I am also curious if it is just better to look at a phylogenetic tree and conclude what is ...
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2answers
36 views

Multiple Alignment cost application

Is there any biological application/case where someone would be interest in the estimated total cost of the alignment between a set of sequences (genes or amino acids) without the aligned sequence ...
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1answer
42 views

What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?

Is there an accepted boundary of the extended major histocompatibility complex (xMHC) in human? Specifically, I am interested in the boundary coordinates for Genome Reference Consortium Human Build 38 ...
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40 views

tissue cross talk using gene expression data

I am studying about tissue cross-talk using gene expression data. My first goal is to identify the genes responsible for communication signaling(cross talk). Let say the tissues are fat and muscle. ...
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1answer
36 views

gene-gene correlation from two different Tissues

I am stuck on how to do correlation for two independent data sets with common row and column names. A and B are datasets that contain as many rows as genes and as many columns as samples. The rows in ...
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2answers
15 views

Easy way to create gene plot in gviz?

I would like to create a simple plot of a given human gene containing the main features, e.g. exons, introns, ORFs, transcripts etc. I understand that gviz is a ...
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1answer
64 views

Choosing Fisher's Exact or Binomial test for overrepresentation in PANTHER

The PANTHER website offers a tool to obtain the GO-based overrepresentation of a gene list (the analyzed list) versus a reference gene list. After entering both these lists, the tool asks to choose ...
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0answers
21 views

GTF parser returned Empty DataFrame

I used the following script to retrieve for RPKM and cov value for each transcript. ...
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1answer
33 views

How to annotate gene length to a list of gene symbols using UCSC data?

I have a list of HGNC gene symbols, I am looking to get the gene length of each gene. Although I also describe these genes with lots of UCSC datasets as features, so I am wondering if there is a ...
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1answer
61 views

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG ...
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1answer
34 views

Seurat DE t.test

I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between ...
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0answers
8 views

How to get the gene names corresponding to genes in a module in R?

On doing module extraction, I get the module as a text file containing the index number of the gene and not the gene names. I have saved the gene names from the original gene expression file in a ...
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1answer
27 views

Comparing gene abundances between metagenomes

My workflow until now: Find fragments of a marker gene in unassembled metagenomes > download and assemble metagenomes > recover the gene neighborhood / gene set of interest Right now I have a ...
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2answers
76 views

How can I obtain a list of all NCBI gene ID's along with their full name, symbol, and also known as symbols?

I would like to do two things: (1) Obtain a list of all NCBI (Entrez) gene ID's. (2) Obtain the "Official Symbol", "Official Full Name", and "Also known as" fields from ...
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2answers
86 views

Problem with merge data while trying to convert gene names in R

I've been trying to code (in R) a way to convert gene accession numbers to gene names (from RNAseq data). I've looked at all the related questions and tried to modify my code such, but for some reason ...
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0answers
31 views

How can I obtain gene lengths programmatically for genes in Wormbase?

I would like to programmatically, in R, obtain gene lengths (excluding introns) of genes of c. elegans given their Wormbase identifier (for example: WBGene00000004). How can I do so?
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41 views

haplotype network analysis in R

it has been a few days that I am struggling to generate haplotype network analysis for a gene plays important role in pesticide renitence. I am trying a R package "pegas" which seem pretty ...
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19 views

Determining a Gene's Unknown Function

I'm a beginner in this field (so pardon my rudimentary knowledge/explanation) trying to understand ways on how I could potentially identify genes of unknown function. I am trying to get as close as I ...
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1answer
33 views

How can I convert codon coordinates to genomic position?

I am looking for a given mutation in IGV, which accepts coordinates in the form of chr<X>:<Y> Where X is the chromosome number and Y is the base ...
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0answers
28 views

miRNA dataset for prediction experiments

I am from the field of Computer Science and I want to perform some experiments related to miRNA and mRNA prediction.I have been searching for datasets in this area and found one called mirWalk ...
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4answers
70 views

Separate multiple sequence into different file, one sequence per file

I have a file contain multiple sequence, and I want to separate them by "gene:" into different file. example: example.fa ...
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0answers
27 views

How do I generate a list of post-synaptic gene markers that will guide me in my search for these markers in intestinal stem cells?

I would like to generate a list of gene markers that represent post-synaptic related genes. I will then use this list to search through single cell sequencing data, in order to assess whether certain ...
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1answer
24 views

Map gene IDs to protein structure if exist

I want to map some gene ids to their proteins structures if they exist. The genes are rows of this CSV. There are other information that may help also such as Product description but that may lead to ...
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24 views

Finding regions between ORFs

I'm doing work on mRNA and need to get predicted mRNA sequences from a genome. I'm working with this genome https://www.ncbi.nlm.nih.gov/nuccore/U00096.3 (E. coli k-12 mg1655). So have a genome ...
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1answer
109 views

How to map gene names to ensembl Ids in R

I am trying to convert a list of gene names into Ensembl IDs but I'm having a bit of trouble. I've tried using the EnsDb.Hsapiens.v86 package but I always get LRG-ID values returned as well, even ...
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1answer
32 views

Assemble reads for a specific gene

I have a lot of unassembled sequencing data and I want to build phylogeny for some genes from these data. I can retrieved the sequene by mapping reads to a reference sequence but if the two species ...
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0answers
18 views

Free, user-friendly software for visualizing and comparing gene clusters?

I'm looking for a tool to do the job listed in the title. I've come across Gene Graphics (https://academic.oup.com/bioinformatics/article/34/8/1406/4708234), but never used it and I was wondering if ...
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1answer
22 views

Available phenotype data from GTEx

I am using gene expression data from the The Genotype-Tissue Expression (GTEx) project, available here: http://gtexportal.org. I would also like to use phenotype data for each sample (especially age, ...
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1answer
43 views

what is the concept of N-channel geneChip?

I can understand two-color and one-color(Channel) gene chip; but there is another type of gene-Chip called "N-channel chips" ; I do not know how can several (> 2) samples be hybridize in one chip. I ...
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36 views

Will using smaller kmers help get larger contigs? If not, then what?

I've been using MEGAHIT to assemble metagenomes, with particular focus on specific genomic areas. Sometimes all I get is gene fragments or pathway fragments (eg. if I know that genes A, B, C, D and E ...
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1answer
36 views

HTSeq-count is returning 0 for every gene, instead of expression value

(Ported from stack overflow) I'm trying to summarize gene count using htseq-count; and it's returning 0 counts at every gene. I'm not sure what I'm doing wrong; I think it has to do with the gene ...
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1answer
19 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 ...
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1answer
189 views

vcf file to gene annotations and or genes

Is there some tool that will convert a vcf/bcf file to some gene annotation, based on the fact that I have the gene annotation of the already exsisting reference genome. Or some tool that will give me ...
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3answers
202 views

What are the different kinds of bioluminescent genes?

I know of the common green glow gene but I forgot the name and I also know that some algae glow blue. There are so many types of bioluminesent organisms, so I am wondering what species have which ...
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18 views

How can I find genes of fundamental metabolic processes for an organism?

I want to find genes of fundamental metabolic processes in the Phytophthora cinnamomi genome. I'm using the genome sequence deposited in the NCBI and I'm searching ORF by ORF, using the ORF finder (...
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0answers
78 views

How to get the GO information for all the human genes?

I would like to retrieve a list of all the human genes and their proteins’ functional classification. The Gene type attribute on ensembl.org is not specific ...
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1answer
33 views

tp53 example in Momand's book

I am new to bioinformatics. While reading Momand's 'Concepts in Bioinformatics and Genomics' , I understood clearly that each codon translates to a specific amino acid. But then, he talks about the ...
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1answer
25 views

How to Convert From Gene Location to SNP Location

I am new to this. I have an SNP array composed of digits [0,1,2] for chromosome 21. How do I find the start:end locations for the region that is "21q22.11" step by step?
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1answer
107 views

Any user friendly way to find rare mutations in whole genome raw?

Is there any user friendly way to find rare mutations in the individual human whole genome sequencing raw data? (from Dante, 30x coverage). To be more specific, I want to find mutations from this ...
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0answers
29 views

How to check the distribution of gene expression across the genome?

I have a group of genes with the same functionality belonging to 3 different families. I would like to see how their expression is distributed across the genome: do they tend to be expressed in a kind ...
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0answers
24 views

Gene size and power of detection in sequence divergence analyses

I want to look at violation of the strict molecular clock and compare dn/ds ratio to test differences in evolutionary rates in a set of genes. Some of these genes are really short (30AA), is it likely ...
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1answer
45 views

correlation between transposon and gene

I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element ...
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1answer
39 views

Download protein structure from gene name

I have a list of gene name, I want to download and save each protein 3D structure corresponding to each gene name.
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1answer
74 views

From ensembl id to protein structure

Forgive me if this question is too trivial. I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this? Is there any script(python, R) so that ...
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2answers
267 views

How can I find out if my gene of interest is duplicated?

To identify homologous genes, I performed tBLASTn analyses against my genome of interest resulting in sequences of a closely related species. Using this method, I found two (and in some cases up to ...
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1answer
76 views

Are there any resources for calculating / representing evolutionary relationships within gene clusters?

I am working with a gene cluster found in several species. The genes involved are pretty much the same, with the odd insertion, but they can be often found in different orientations. So, I can't just ...
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2answers
98 views

How to efficiently get human gene names from NCBI based on a large list of SNPs

I found a good answer related to my question here: How to get a list of genes corresponding to the list of SNPs (rs ids)? But it says about small number of SNPs. I want to get gene names based on ...
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0answers
71 views

Visualizing Ortholog and Paralog genes

I ran PorthoMCL but I could not find an explanation about the output format and I would like to visualise the results, maybe as a circos plot. PorthoMCL produces two output files: Orthologs sample ...
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3answers
781 views

CDS length for each human gene

Does anyone know where and how could I download a list of all human genes and the length of the coding sequence for each gene? Is it possible to do this on the NCBI site, ensembl?
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0answers
37 views

Building cancer gene database

I am trying to build a database of different cancer genes i.e lung cancer, throat cancer etc. Searched through NCBI website by searching for nucleotide sequences, but I am unable to find appropriate ...