Questions tagged [gene]
Use this tag to refer to the gene sequence/coding part of the sequence.
201 questions
3 votes
2 answers
89 views
How to calculate the genomic position of a variant?
Student here. The variant c.467C>T on GRCh38, transcript NM_020469.3, on Exon 7 from ABO is supposed to be 467 positions within the coding region of the gene. I need the genomic position for this ...
2 votes
1 answer
91 views
How do I count the number of genes per contig or scaffold from a gff file?
I annotated my genome, and I used different datasets and I got a different number of genes each time. I obtained a GFF with EviAnn, and want to compare the annotations based on the number of genes per ...
- 23
2 votes
0 answers
51 views
Which other population group is genetically closest to the Yamato Japanese?
Here is the full question that I want an answer for: "Which population is most genetically similar to the present-day Yamato Japanese people? The present-day half-Yamato-Japanese, half-European-...
- 21
0 votes
1 answer
64 views
Modelling RNA translation
Are there formal or computational models of RNA translation that treat codons as virtual instructions in a ROM-like lookup table architecture? I’m exploring analogies between embedded systems and ...
user23998
1 vote
2 answers
73 views
Will Cytoscape allow me to draw a network piece by piece and test claimed interactions?
As a scientific editor, I sometimes need to envisage proposed gene–enzyme–metabolite networks while editing papers. Being a visual thinker, I have to plot the claimed interactions and effects (as ...
- 11
2 votes
0 answers
40 views
BEAST Low Posterior ESS and Posterior Support Values for MCC nodes
I've been working with BEAST for the past couple weeks to try to make a comprehensive phylogeny of 16S for a genus of frogs. There are two groups of interest to me: the mainland clade and the ...
0 votes
0 answers
43 views
Downloading Bulk Gene data from GeneALacart
Does anybody knows about downloading gene data information via GeneALacart .or any database contains curated gene-disease-pathway informations .
- 1
0 votes
0 answers
31 views
Panther overrepresentation test results interpretation
Could you suggest a tutorial or a publication providing example how to interpret, making sense of panther overrepresentation test results? A little DOI could save my life. I have a list of regulator ...
1 vote
0 answers
33 views
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 ...
- 11
0 votes
2 answers
101 views
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 ...
1 vote
0 answers
33 views
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 ...
- 11
1 vote
0 answers
38 views
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 ...
- 11
0 votes
1 answer
37 views
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
1 vote
1 answer
75 views
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 ...
0 votes
1 answer
265 views
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