Questions tagged [gene]
Use this tag to refer to the gene sequence/coding part of the sequence.
196 questions
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How to find hub genes when your input DEGs are more than 4000 because it takes so long to calculate modules
I tried extracting 250 hub genes from 4750 DEGs, but it takes too much time while calculating modules from 11 methods and coudn't proceed further.
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Metabolite function from DNA sequences
I have an aligned metagenome fasta file. I want to see the relation between the aligned genes and the so-called Clusters of Orthologous Groups (COGs). For the purpose of the analysis I am using the ...
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13
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Finding DB with biological pathways and related pathways
im looking for a DB that given a biological pathway or gene set, can provide other biological pathways that are related to it, either by gene overlap or by interacting in a given process. Kegg ...
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2
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31
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Finding gene duplications in bacteria
I would like to know if there is an easy tool to find how many copies of a certain gene are present in all available bacterial genomes.
For example, which bacterial genomes contain one or more copies ...
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15
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Pathway enrichment analysis - minimum amount of proteins?
I have 6 proteins significantly associated with an outcome and have done a pathway enrichment analysis (PEA) with them (in both Enrichr and R with the same outcome). However, I wonder if that is too ...
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enrichKegg arbitrarily excluding certain genes from gene set during analysis
I'm using the R-package enrichKEGG to perform an enrichment analysis on a vector of genes. As output I get a list of pathways containing some number of the genes in my vector. In the results there is ...
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14
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Cannot invoke "Object.toString()" but Uniprot IDs are there
I'm trying to stringify my gene network in Cytoscape and have designated a column with uniprot IDs for the basis of the search. Not every gene has a uniprot ID but I have selected to retain genes ...
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1
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22
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Identifying Accurate Exon Boundaries for Highly Polymorphic Exon 2 in MHC Class II Beta Gene
I am working on annotating the MHC class II beta gene in a bird species and need some assistance in determining the correct splice sites for exon 2. The sequences I obtained seem to work with multiple ...
user21035
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42
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Edge table on cytoscape won't show gene name on the shared name pp interaction column
Could you help me solve this problem?
So, basically both shared name and name column on this edge table not showing the gene name. It just show like this picture.
How can I change the name in the name ...
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1
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96
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Stringapp failed to start in cytoscape
Hello, I encountered a problem of stringapp failed to start. I already reinstall string app 3x but still unable to use string app for creating network of genes.
Thank you
Vania
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"BLASTx for miRNA Annotation: Mature vs. Primary miRNAs as Query Sequences"
I am doing miRNA annotation of a plant genome. I have two files - one containing all the predicted mature miRNAs and another containing all the predicted primary miRNAs. I want to find out which are ...
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StringApp installed on Cytoscape, But does not added to IMPORT/Network from Public Database
I have different versions of Cytoscape in different PCs. one is 3.10.1 and the other is 3.10.2. for both I installed StringApp but in 3.10.2, It is not added to "import/network from public DB&...
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Find most abundant transcript isoform of a gene across different tissues in long read RNA-Seq data
I want to understand which is the most abundant variant of a gene of interest across different tissues by looking at different publicly available databases (mouse/human). I have deduced from ...
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2
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190
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What is difference between gene and CDS in the gff file?
I'm investigating bacterial genome.
In GFF file, it includes gene, CDS, tRNA or something like that in region fields.
What is the difference between gene and CDS?
Thant you in advance.
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Best reference book for basic concepts when working with bioinformatics
I'm starting to study Bioinformatics, I already have basic knowledge of Biochemistry and Genetics, but I want to buy a reference book, to use when I forget a concept (I'm a Computer Science student, ...
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453
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What is it about gene names starting with "LOC"?
I was struggling to use AnnotationDbi to change my ensemble ID to gene name, for datasets of three different species (human, canine, mouse). Among gene names for all three species there are genes with ...
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Gene ensemble vs Hugo id
Hi
I have been recently struggling with the gene annotations and changing gene ID to ensemble ID. While I was doing that there were some genes for the same species that had the same gene ID but ...
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1
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76
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conducting a ttest on a board of 1000 genes in 50 peope divided into to groups(A and B). pvalues are different each time
I am struggling in conducting at test on a board of 1000 genes in 50 individuals divided into to groups (A and B). I have a dataset of 1000 genes of two groups of people (total individuals=50)
group A ...
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82
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Convert genotyping results to vcf or other plink formats
I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can ...
2
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1
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74
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How to rearrange gene ontology obo file?
I have a gene ontology obo file, and would like to rearrange the obo format file in a single column to a text file in three columns comprised of 'parent (id:GO:xxxxxxx)', 'child (is_a: GO:xxxxxxx, ...
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59
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Gene Set Comparison Without Expression Data
I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated ...
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2
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73
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Extract data from genome
This question was also asked on Biostars 3 months ago, i.e. a long time - so its perfectly reasonable for the question to be asked here
I started studying bioinformatics and I enjoy it a lot (I'm a ...
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2
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179
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How to get the nucleotide sequence for protein NCBI accession code, programatically?
It is a lot easier in my work to do blast searches against protein databases when I can, since I work with distantly related organisms. But sometimes, I need to work with the actual nucleotide ...
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How can I calculate the coverage of a gene in exome sequencing / calculate coverage per gene?
I have a bam file of whole exome human data. I now want to check coverage of a list of genes in my data. Basically, I want to get output like, for example:
...
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66
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Custom-made kraken2 catalogue
I am looking for instructions on creating a custom-made kraken2 catalogue from the sequences of my choice and the corresponding phylogenetic tree in newick notation.
I will appreciate an input on ...
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67
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SKAT method in R
I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene.
...
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1
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157
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Is my reference sequence too small?
I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I ...
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256
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Converting a Dante Lab VCF file
Is there an easy way to grab the rsids (hg38) of a VCF file? I know one of the tabs can contain RSIDs, but this file doesn't contain any.
I have a software I created for mapping 23AndMe DTC testing to ...
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1
answer
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Getting nearest gene from SNP data using SNP ID, CHR, and BP
I have data from a GWAS that provides me with the SNP, Chromosome, and base-pair. My data set has thousands of SNPs. What is the easiest way to find the nearest gene for each SNP using this ...
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154
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How to get a file with the introns of a gene?
I was able to get the exons of a particular gene as a fasta file from the NCBI genome viewer. As for introns I only found a bed file that showed where the intron starts and ends, along with its ...
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78
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Availability of information on genes in Gnomad VCF data
I was wondering does the gnomad genome data that is downloaded in the vcf format on variants contain information on what is the nearest gene and is the genomic location available exome/intron?
if yes ...
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76
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Mismatch between mutant gene and reference gene outside the site of mutation
I am tasked with designing primers for a particular mutant (Target Gene Locus: At1g28490 i.e. SYP61) of Arabidopsis, obtained from Gabi-Kat:
The NCBI reference sequence for the genome goes:
...
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62
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SNPs location out side the gene
I downloaded exome data from gnomad to get the allele frequency of some SNPs that I'm analyzing. The SNPs are from external resource. Some SNPs (in my data) are not present in the exome data (in ...
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What visualization was used for ICA in the tissue experiment?
I want to run the experiments in mentioned in enter the matrix.
For the the plot in figure 3B it mentioned that
The relative absolute value of the magnitude of each element in the
pattern matrix ...
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150
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Why are genetic algorithm chromosomes represented using 8 bit binary?
I am learning about genetic algorithms.
Why chromosomes are represented using 8 bit binary.
This arose when I apply crossover techniques to the bits.
Please help me to find the answer.Thanks in ...
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2
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381
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Searching for HLA-B in DNA results
I'm trying to find the HLA-B*15:01 variant in my DNA results, prompted from this research paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8142661/#:~:text=HLA%2DB*15%3A01%20is%20strongly%...
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Comparing common genes and transcripts between Gencode and Refseq
This is a very naive question - I am trying to compare and get the common lncRNA genes and transcripts between Gencode and Refseq from their gff files.
Since their gene_id, gene_names are different, ...
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48
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Building a group representation of genes' ontologies
I have a list of genes (about 2000) from lines of drosophila subobscura, in the following format:
LOC117900589
LOC11788959
LOC11790331
I'm trying to represent this set of genes in a useful way.
So, ...
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641
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Error of duplicated rownames although there are no duplicates
I have a data frame that I want to switch its row names from EnsembleID (GENEID) to gene symbol (SYMBOL). When I try to switch, I get this error:
...
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147
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snpEff annotation and variant in a gene
I'm using snpEff to annotate genetic variants. However, the annotation often returns more than one annotation (see below for an example):
...
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Which components must be included in the HDR plasmid?
I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues.
I wanted to know exactly which components must be included in the plasmid.
I know that I have ...
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65
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Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?
When we use antismash command with the genome sequence file as follows:
antismash GCA_002095535.1_ASM209553v1_genomic.gbff
it screens the genome for all the ...
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How good does the assembly of an NCBI prokaryotic genome have to be in order to argue gene loss?
NCBI has several labels for assembly completeness - Complete, Scaffold, Chromosome and Contig. Complete would be a circularized genome (or linear, rarely)
For a Complete genome it's fairly ...
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498
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Converting .bw files to .fq (fastq)
I am able to convert .bw files to .fq(fastq) manually in Shell, but I would like to automate the process coz I have hundreds of .bw file that I need to convert. Till now, I could think of following ...
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516
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VCF or BAM file for raw data of gene test?
My friend has a VUS (Polymicrogyria with or without VEDS) mutation that was found in her whole-exome sequencing with respect to the phenotype given that time. At present, her doctors have more ...
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1
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56
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Target genes for piRNA
Where I can find a database or tool to give me the target genes of PIWI (piRNAs) in human?
I found one but works for worm like <...
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100
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Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?
I need to know whether my pan-genome is open or closed. For that, I need to calculate the ...
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47
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How to summarize multiple exon copy numbers into copy number of the corresponding gene
I have a matrix, sample by exon, containing a copy number value for each pair (sample, exon). I would like to generate a second matrix, sample by gene, where the copy number of the exons is ...
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48
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Is there a publication database or search engine offering geneID or UniProtID correlation?
Do we have a publication database or search engine that offers geneID or UniProtID correlation?
For example, I search "IPS cells" -> I want to know what genes or proteins are under active ...
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How to get a list of all human morphogens?
Gene Ontology provides many genes annotated as taking part in various morphogenesis processes but I want to get a list of all morphogen coding genes specifically. Uniprot does not have "...
