Questions tagged [bioinformatics]

The science of collecting and analyzing complex biological data such as genetic codes using informatics.

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10 views

Term for context based behavior?

Is there term in neuroscience that describes change in neuronal circuits depending on context: low sugar/fear/... => hormones => different pathways of behavior ...? I know that is something from ...
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75 views

What exactly is “chromosome topology”?

I've been reading a lot about Hi-C lately, and this has been bothering me. So far as I can tell from reading around, the topology is related to the conformation of the linear chromosome. This seems ...
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51 views

Is there a negative correlation between the mRNA produced by the cell and the time of extraction? [closed]

I am doing some data analysis about gene expression time series. When I plot mRNA produced by P. Furiosus cells irradiated by gamma radiation against the time of extraction, it seems that there is a ...
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23 views

What does an allele frequency of 0 mean in gnomAD v3?

There is a single nucleotide variant: 18-47394-G-A (GRCh38) with an allele count and allele frequency of 0. As I understand it, this means that there are no alleles in the population with this variant,...
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14 views

What is the best way to find which domains in a list of InterPro IDs are catalytic?

What is the best way to find which domains in a list of InterPro IDs are catalytic? (In this case, we are looking at human enzymes and their domains' InterPro IDs.) Thanks in advance! Setz
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69 views

Rigorous definition of the kinship coefficient and proof of a recursion thereof

I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...
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1answer
50 views

Why do doctors reccommend vegetable oils in high cholesterol and cardiovascular disease?

As there is high cholesterol in body why the patient need more fats and why the doctors are recommending it Transcribed: Vegetable oils are rich in polyunsaturated fatty acids (PUFA). The fatty acids ...
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Is there a way for POPart to accept indels in chloroplastidial genes?

I need to construct a network concerning chloroplastidial genes using POPart. My problem is that POPart does not know how to deal with indels. I have already coded them using SeqState (simple indel ...
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30 views

Help Finding Specific BlaZ Gene Type Sequences on Genbank

I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that ...
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1answer
61 views

What is the energy required for storing and performing computations in synthetic computational biological cells?

I want to know the energy costs of various computations performed through synthetic biological circuits in terms of ATP. I am primarily interested in storing of bits, addition, and multiplication ...
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Examining antibody - target interactions in PyMOL

I'm a student currently looking at antibody responses against a viral target protein of interest. I have my own, annotated PyMOL session of my protein and I also have .pdbs of crystallised antibody ...
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Metrics to analyze branch lengths in phylogenetic trees

I'm interested know about some basic metrics that could be used to discriminate trees based on their branch lengths. I know of branch length unaware topological/tree shape-based methods such as ...
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53 views

BLAST, using Smith-Waterman in the last step and S-score

In my bioinformatics course we studied the BLAST agorithm. After finding the HSP's and joining the HSPs together that are close enough and in a correct diagonal trend, we perform a next step: namely a ...
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1answer
20 views

What is multiplet nuclei capture rate?

I met this terminology in a publication.https://core.ac.uk/download/pdf/226940818.pdf. It's in the last sentence of the second paragraph in the text. I tried to search for it but didn't get a ...
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1answer
26 views

Why the major gene model can be supported by finding de novo mutations in affected cases?

I found a sentence which I can't fully understand in a publication on the genetics of autism. The unified major gene model is supported by the significant increase in damaging de novo mutations ...
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1answer
46 views

How to download omic data from ncbi? (SRA data or any suggestion?)

I proposed myself to replicate the results in this paper with an accession number PRJNA325650. So, I'm trying to download the data. Which will be the best way to do this?. I tried with the sratoolkit, ...
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22 views

Assessing beta diversity variations with time

I'm just starting in the field of ecological statistical analysis and I have a few doubts regarding a dataset that I'm working on. The dataset is composed of several samples collected at a single ...
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26 views

Who define the SARS-CoV-2 haplotypes?

If you look in this paper https://www.nejm.org/doi/full/10.1056/NEJMoa2006100 they work with several haplotypes of the virus. They claim that the definitions of the haplotypes come from GISAID/...
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Question about Interpreting from IGV

Hello I am a complete beginner with zero knowledge of bioinformatics taking a class on it offered by my dept. I have a screenshot of my IGV of 5 genes that I used from human genome 38. I simply ...
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How large a part of the corona-virus is coding?

If you find an example of a sequenced string of coronavirus it is about 30.000 long. Looking for example here https://nextstrain.org/ncov/europe you'll see that by far the largest part of this is ...
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1answer
41 views

blast search against UNIPROT

I would like to ask how i can search in blast against UNIPROT (TREMBL PLUS SWISSPROT) for a selected organism. In the BLAST site there is no option about UNIPROT(only Swissprot), and in the uniprot ...
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Lineage inference based on N randomly partitioned copies of a gene

I am interested in reconstructing cell lineages based on the sequences of randomly partitioning plasmids. I can find lots of models to build lineages based on a single sequence (e.g. bacterial gene) ...
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I just had my genome sequenced. Can someone tell me what these different file formats are?

I just had my whole genome sequenced and now I want to play a bit with bio-informatics. However, the documentation is quite scarce on the file standards used. These are the files I have been given (...
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2answers
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How can I classify the 3 clades(S, G, V) of the coronavirus that are found on GISAID?

On GISAID they classified the corona using 4 clades(S, G, V, Other). I would like to know exactly how these genomes were classified for my research. So how do you classify a coronavirus genome as ...
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3answers
165 views

Where are there analyzable signed directed network datasets?

I'm looking for biological datasets with specific properties that are available for me to analyze. Informally put, I have a hammer and I am looking for a nail. That is to say, I have an algorithm and ...
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1answer
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Relationship of RNA-binding proteins to peptidyl-prolyl cis-trans isomerase [closed]

I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?
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80 views

Extract mutations from fasta sequences

I have a large amount of protein sequences in the .fasta format and I would like to extract only the amino acid mutations from these sequences, so that, in the end, I want to have a list that looks ...
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Which molecular dynamic simulation software is more applicable for protein and large-area surface interaction simulation? And how to run it?

I am trying to do the molecular dynamic simulation for protein-surface interaction, the surface (like cellulose or PET) is a film-like or crystalline material with large surface area, I had tried ...
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1answer
196 views

Where can I find the genome of the L-strain coronavirus and the S-strain coronavirus?

I read an interesting article about two strains of the coronavirus: https://www.newscientist.com/article/2236544-coronavirus-are-there-two-strains-and-is-one-more-deadly/ I would like to know how the ...
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Can non-directional and bi-directional features be described in genbank format?

I'm just wondering if there is a standard way within genbank files (.gb) to specify that a feature is non-directional or bi-directional. I don't see any info on the https://www.ncbi.nlm.nih.gov/...
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28 views

In the notch signaling pathway, what is Fringe activating?

Take a look at the notch signaling pathway in human from KEGG : https://www.genome.jp/kegg-bin/show_pathway?hsa04330 I want to know what is Fringe activating. It is not pointing to another gene or ...
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Outlining cell edges of an epithelium

Is there any free software (for Windows, preferably) to detect cell edges in pictures of an epithelium, for example? I know Packing Analyzer does this, any other suggestions? Ideally, I would like ...
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1answer
151 views

How to do research in bioinformatics without wet lab experiments?

I graduated in physics from Bangladesh and keen to work in the field of biology. Like, systems biology, computational biology, bioinformatics or systems medicine. I have not produced any research work ...
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26 views

Why use log odds and not probability to construct substitution matrices?

I'm studying "Understanding Bioinformatics" by Marketa Zvelebil. I came to know that substitution matrices (PAM, BLOSUM etc) use log odds and my immediate thought was why not use probabilities. ...
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Mendelian randomisation and covariates

I am using a mendelian randomisation (MR) approach to determine whether there is a causal effect of an exposure X on the outcome Y. To do so, I run a genome-wide association study (GWAS) of the ...
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26 views

Trying to understand PAM matrices

If I have several PAM matrices all computed using different evolutionary distances, and I compute the score between two amino acid sequences, is the max score I get using any one PAM matrix the most ...
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1answer
21 views

Is there a difference between splice-site mutations, and non-stop mutations

I'm working on a bioinformatics project where a lot of the biology I've had to learn from scratch. From my current understanding, a non-stop mutation alters a stop codon such that the transcription ...
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1answer
42 views

What is the technical term for when a clade on a phylogenetic tree does not have an extended branch? (see image)

As we see with ZCA2, ECA2 & XCA2 these branches are compressed and do not extend as TCA does. Is there a technical term for this and what usually causes it?
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387 views

How many atoms has the smallest known bacterium? [closed]

Background thoughts before this question: is it feasible to simulate a complete bacterium, atom by atom, in a computer simulation? On modern systems, either in an upcoming exascale computer? In ...
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3answers
86 views

What tool can I use to align multiple protein sequences to one reference sequence?

I have a protein of interest which is ~300 amino acids in length. I also have around 40 short sequences (all 9 amino acids in length); these are all very different from each other. I would like to ...
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54 views

Can two proteins activate/inhibit the same gene at the same time?

Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right? So if one protein has already inhibited that gene before ...
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1answer
38 views

Where to find a list of genes coding for protein in human

I have raw read counts extracted by htseq from STAR alignment I have both data with both Ensembl IDs and gene symbols, but I need only a latest list of protein coding genes in human; I googled but I ...
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1answer
60 views

Help on selecting 2 tests - unsure if they are paired or non-paired statistical test

I have data that measures the temperature of flowers and leaves on different plant species. These are the comparisons I am trying to make: Comparing the flower and leaf of the same plant at the same ...
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55 views

What are the methods for detecting anagenetic versus cladogenetic change?

I'm new to the study of phylogenetics and am wondering if there are ways of identifying evolutionary changes that associate with cladogenetic events versus those that arise via anagenesis.
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38 views

Is there a system biology approach to compare pathways or famillies of proteins from an evolutionary point of view for the same organism?

I would be interested to know if there is a method/analysis or a set of methods to compare two groups of pathways or families of proteins. I would specifically be interested by a system biology ...
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1answer
56 views

Where can I obtain the sequence of the E. coli ribosomal RNA precursor?

I have found separate sequences for 16S rRNA (from the small subunit) and 23S rRNA and 5S rRNA (from the large subunit). I need the full precursor rRNA sequence, which I cannot find. However the ...
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46 views

How accurate are Illumina microarray chips for genotyping?

What is the error rate for these machines in genotyping (like for 23&me)? What is the chance of a false positive or false negative?
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48 views

How to reduce the number of sequences in a Multiple Sequence Alignment?

I have a Multiple Sequence Alignment, where there are around 5000 sequences. There also exists many sequences where, there are so much of non-sequenced regions (for instance, AU----CGGGCA--NNNNNNNNNN)....
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18 views

semantic similarity measurement for cell line ontologies

I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies. The problem I have is that I have found a Python library called Fastsemsim, but it ...
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52 views

Proteomics data Vs Transcriptomics data?

I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...

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