Questions tagged [bioinformatics]
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
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Assoc. between drug-induced perturbations and disease processes
I'm trying to understand the main idea of this paper: https://doi.org/10.1038/s41467-021-21330-0
A news link: https://www.azorobotics.com/News.aspx?newsID=12055
As far as I understand, they have the ...
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1answer
39 views
Does gene isoform have different genetic location?
I would like to understand how a gene is assigned to a specific coordinate (e.g. NOC2L Chr1 879583(Start) 894679(End)). Next, let's say NOC2L gene has a few different isoforms, do those isoforms ...
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29 views
Differentiating molecules based on peptide sequence? How to annotate?
I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain ...
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63 views
What does does a blood sample tell you about an individual's identity?
I am working on a fiction/mystery scene where blood is found in a particular character's residence but the character themselves is missing. I would like to understand whether the law enforcement/...
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1answer
80 views
Does anyone have a tutorial or some guide to get started with Rosetta protein modeling and design tool? (I am a Mac user) [closed]
I have been trying to get started with Rosetta protein modeling and design software bundle. I searched online but the tutorials in the Rosetta website are difficult follow. I have the binaries already ...
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28 views
Evidences supporting that coronavirus (SARS-CoV-2) came from bats
I was trying to find evidence that the coronavirus (SARS-CoV-2) came from bats. So far I know that coronavirus shared 96.2% overall genome sequence identity with a bat coronavirus RaTG13 from ...
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1answer
107 views
Get “DNA” of one parent based on its children [closed]
I'm no biology expert so bear with me, but I've been given a task to estimate alleles of an animal based on the animal's children and the children's other parents.
I've looked up Mendel's laws but I'm ...
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1answer
46 views
Finding All of the Genes in a given Genome
I'm interested in finding the start position of each nucleotide in a given genome. I first went to EcoCyc and wrote a scraping script for their E coli data, but I can't find the same web page layout ...
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45 views
What are the advantages of long read sequencing for cancer oncogenomic research?
Currently I am using whole genome nanopore sequencing, Illumina short read and 10x linked read to study oncogenesis mechanisms of certain types of rare cancer. I am wondering about the advantages of ...
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77 views
Poly-G tails in NovaSeq Paired-end sequencing from museum samples
I'm currently working with DNA samples originating from museum specimens, this means they have been stored in formaldehyde for the last 50-100 years.
The DNA I'm analysing has been sequenced by ...
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24 views
Why certain COGs appears more often in Humans Bacteria but not in plants Bacteria
I'm doing a Bioinformatic project from the university where I got a DB of COGS from Human & Plants Bacteria genomes and I need to find distinguishing sets in this DB and explain the biological ...
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1answer
31 views
Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?
I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is ...
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36 views
Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software
I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have ...
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22 views
Creating a phylogenetic tree from my selected publicly-available sequences (WGS) in NCBI
I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic ...
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1answer
33 views
Would there be more amino acid residues in the extracellular or intercellular space?
I am working on a bioinformatics project with HMMs and want to write some initiation probabilities for the location of amino acid residues. I know for different transmembrane proteins there will be ...
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1answer
80 views
How to identify an unknown species from a .fasta file containing its genome sequences [closed]
I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole.
I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) ...
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1answer
36 views
DNA extraction kit for microbial mats, rocks, and soil in a remote area
I am hoping to perform a metagenomics study of samples from a lava tube. It will be in a remote area (with no large scientific equipment) and I would need to bring all scientific equipment myself. For ...
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38 views
NCBI blast for exact match of short sequence
I'm trying to Blast for exact matches to the sequence: 'ATTGNNNNGCAAACCA' in the human transcriptome using NCBI Blast on its 'refseq_rna' database. However, when I do a basic query I get "No ...
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13 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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2answers
111 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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1answer
53 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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30 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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1answer
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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1answer
77 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
84 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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24 views
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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1answer
52 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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2answers
92 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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1answer
34 views
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 ...
2
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2answers
41 views
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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1answer
58 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
25 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
29 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
80 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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2answers
27 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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1answer
82 views
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
46 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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1answer
4k views
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
62 views
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
214 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
21 views
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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103 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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1answer
204 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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1answer
29 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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1answer
205 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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1answer
23 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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1answer
896 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
278 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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0answers
55 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 ...
