Questions tagged [bioinformatics]
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
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Biological mechanisms plausible for Kalman filtration (or some other)
I want to find out if there are mechanisms for filtering navigation information similar to Kalman filtering (or another) in the life of living beings, the structure and functioning of organs designed ...
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Molecular Docking - a guide
I have a question regarding molecular docking, as I am far for familiar with it.
I started with generating the models of a ligand (which is a F(ab) part of an antibody).
I obtained the structure of a ...
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Extracting amino acid sequence from WGS data
I would like to know, given a dataset of WGS data, what tools can I use to identify the coding regions within the DNA sequence and then convert them into amino acid sequences?
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Do fruits have fingerprints: Can a fruit (say mango) be identified uniquely by some characteristics?
I am not a biology/botany person, so pls excuse me.
Context as asked in comments.
I want to track a fruit from the time it was plucked out of tree to the time it reaches in the hands of customer. Can ...
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Export AlphaFold Server file and visualize on PyMol
I am currently working with AlphaFold Server, which is Google DeepMind's public access release of AlphaFold3, a model for biomolecule structure prediction.
I am using it in order to predict protein-...
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What is the probability distribution of a neutral mutation's allele frequency after k-generations? (in asexually reproducing organisms)
I've had trouble finding info on how to model this problem, so figured I'd ask it here. I'm trying to figure out what the probability distribution is of the frequency of a mutation in a population ...
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What is the reason for the discrepancy between the total number of non-N bases and the total length of the human genome assembly on the NCBI website?
I've been digging into the human genome assembly data and I've stumbled upon a discrepancy that I couldn't resolve on my own. I'd appreciate any insights or explanations from the biology community.
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Rectangle-like structures and their folding in biology
I've heard that mathematics helps to explain some biological problem. For example gömböc, which was a well hidden body from mathematicians, explains the body structure of some tortoises in relation to ...
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How is the "global pLDDT" score in the Protein Data Bank calculated?
Consider this list of entries for the Tobacco Mosaic Virus (TMV). I selected to sort by 'Global pLDDT' from best to worst. It is my understanding that pLDDT is usually calculated per residue for a ...
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Best way to predict the effects of deletion mutations on protein function?
I have the coding sequences of a WT gene and several mutants of this gene (deletion mutations varying from 5bp to 50% of the sequence deleted). What is the best method for inferring the impact of ...
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Peptide fragment software in mass spectrometry
I am trying to study peptide fragmentation in mass spectrometry.
My goal is to find software with which I can retrieve the molecular structure of the peptide and see the a,b,c fragments.
I found these ...
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Extremophile hunting and identifying unknown microbes
I'm going extremophile hunting! We're doing a trek by boat between some islands with semi-active volcanic terrain to try to document some interesting species, and running into a problem I've never ...
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BLASTN in NCBI strand Plus/Minus
I am a newbie in Bioinformatics. I am trying to understand terminologies used in NCBI BLAST system. Here is what I am trying to align:
So effectively I am trying to align two sequences with the ...
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How does one determine what sequencing coverage/depth to use?
In the context of rare diseases, what sequencing coverage will be sufficient to detect the mutated loci (for eg. SMN1, SMN2 CNVs, gene SNPS, INDELs etc) ? How does this relate to statistics and how ...
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Clustering collection of PDB files based on 3 dimensional structural similarity in python
I have generated a set of 3-dimensional structures of the peptide AGAGAG with different structures. Total number of PDB files are 300. I need to cluster the peptide structures based on their ...
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Is there no good way to run the Vienna RNA tools on Windows?
I'm trying to get the Vienna RNA tools (particularly RNAfold) running locally (as opposed to using the web interface--because I have lots of sequences I wish to process in batch mode). On the website, ...
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Is it possible to proccess human genome in a local computer?
I have some basic programming knowledge, and I would like to take a look at my genome and search for specific sequences related to mental illness and addiction.
The test costs only 1000$ in Spain and ...
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Quantifying Hydrophobicity from amino acid sequence
fourth-year undergrad here so any help is super appreciated! Also this is not something I am working on for a grade, so pls don't think I am just looking for someone to do my homework lol!
In a gist, ...
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How to convert Kilo Units (KU) to mg? [duplicate]
Im searching for AChE (Acetylcholinesterase) and on sigma-aldrich it is showing 2 KU or 2000U/mg of protein and on MedChemExpress it is showing 50mg then how can we calcute how much will be the drug ...
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Database or model for plant nutrient requirements with respect to soil and climate?
Microalgae are organisms that can grow in aquatic environments and use light and carbon dioxide (CO2) to create biomass. Research showed that Microalgae biomass can be used as a bio-fertilizer.
My ...
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Datasets for Genetic Diversity of Species Across Geographical Distribution
I'm carrying out some research on applying machine learning methods to ecology and conservation. I'd like to know: are there some datasets on genetic diversity across geographical positions? ...
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Compute a melting temperature in viennaRNA?
Posting here to get views, but may be more appropriate for bioinformatics or chemistry SE.
There are a variety of utilities such as biopython or primer3 that compute melting temperatures.
However, ...
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Can We Determine the Cell Types Ab initio?
Is it possible to find all cell types in the human body and their respective transcriptomes by analyzing the human genome (and doing no physical experiment)?
If such a thing is possible in principle, ...
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TMPRSS2 Primer Design
I am trying to design a primer for TMPRSS2 PCR reaction. However, this gene is in reverse position like in the picture I'll show.
From the nucleotide sequence I got from NCBI, should I reverse the ...
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Questions about ChIP-seq reads and MACS
I had a few questions raised by the below diagram in relation to how ChIP-seq reads look like (source). I would be very grateful for your insight on them!
From the below diagram, it seems that, in a ...
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Cross correlation metric in ChIP-seq experiments
I found this explanation of cross-correlation metric in ChIP-seq.
Now, the definition of Pearson's correlation coefficient between two random variables $X$ and $Y$ is $$\rho_x = \frac{Cov(X,Y)}{\...
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Can changes of transposable elements in Drosophila be detected using RNA-Seq?
Not sure if this is the right forum for such a question, but please refer me to the correct one, if possible.
Does anyone has experience in working and detecting transposable elements using High-...
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Aligning two PDB structures with different numbers of atoms
What options do I have to align two PDB-files of ribosomes but with different number of atoms? I need to do the alignment using selection "name CA or name P", because the ribosome has both ...
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What does it mean to collapse heterozygous alleles?
I am a bioinformatics rookie. I read a paper, it said:
existing algorithms either collapse heterozygous alleles into one
consensus copy or fail to cleanly separate the haplotypes to produce
high-...
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Defining cell state and type without calculating distances in expression space
Usually, cell types are found by clustering cells in expression space (or some lower dim. projection of it), and calculating differentially expressed (DE) genes. These DE genes are then used to ...
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Variant Allele Frequency (VAF) peaks for clonal CNAs
I am reading an overview of the CNAqc package, which defines how the algorithm computes "Variant Allele Frequency (VAF) peaks for clonal CNAs."
mutations present in a percentage $0<c<...
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How to make predictions on genes not involved in a particular disease
I have one set of genes which counts about 100 such that every gene of that set is evidence based involved in a particular disease. Let's call this set A. For a machine learning project I need a set ...
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Suggestion on program/algorithm to segment nuclei
I've got some images such as the one in this post, obtained from the neuroepithelium of a chick embryo in a confocal microscope, where nuclei have been fluorescently labeled. I'd like to be able to ...
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How do genetic variants of a gene moderate an association, leading to counterintuitive result?
I have run moderation analysis to study the interaction between SNP (dominant model) of a gene (A) with DNA methylation on cognition measures. For this, I have calculated the mean DNA methylation ...
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Alignment given two sequence
I have two sequences and I need to perform sequence alignment to determine all possible sequence alignments. I have created the matrix and managed to find 16 alignments.
I wanted to understand if I ...
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How to look for different transcripts for a protein?
I am trying to find all the different transcripts for a protein that translate into different isoforms of the protein.
However, when I look it up online, there is no clear organized data on different ...
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How can I find/simulate mixed-ancestry DNA data?
Some collaborators and I are building an ancestral inference tool, and we're having trouble obtaining reliable ground-truth data for samples of mixed ancestry. All the ground-truth DNA datasets we're ...
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Making sense of infinite-sites mutation but finite-sites recombination coalescent simulator
Hudson (1983) introduced a coalescent simulator with infinite-sites mutations and finite-sites recombination. This seems paradoxical because the documentation of the simulator (section on crossing ...
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Simulate merging of two ssDNA together
I have two .pdb files with two ssDNAs, which should form some specific shape when closed together. Is it possible to model/simulate this merging somehow?
I would preferably like to have a program that ...
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Is it possible to identify secreted metabolites or secondary metabolites from a gene list?
So I have a gene list obtained from differential gene expression analysis of a metabolic disease model, and I was wondering if I can identify metabolites or secondary metabolites that may be produced ...
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what are the nodes and edges in gene regulatory networks
I am trying to find out how one can using gene expression data can infer gene regulatory network applying graph theory concepts. But I could not find a proper reference that
1)explain how one can get ...
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What do the colors mean in representations of amino acids?
I've seen sequences of amino acids depicted using colors, which I imagine correspond to whether the side chain is charged, etc. I can't figure this out, though, and I'm not a biologist or biochemist. ...
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Are there any biometrics that can measure tiredness (sleepiness)?
Are there any biometrics that can estimate how tired someone is? I specifically refer to tiredness in the sense of sleepiness (as opposed to physical tiredness that might happen after a workout, for ...
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How to align more than 2 sequences with Needleman-Wunsch?
I have a DNA sequence of a protein and around 1200 zinc finger target sequences. These zinc finger target sequences are 9 bp long, resulting in BLASTn not finding them in the sequence. Needleman-...
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Transcript without a start codon in mouse genome?
I am looking at the mouse reference genome in combination with ensemble annotation and am finding many transcripts that have no start codon.
For example, the transcript ENSMUST00000193149 at position ...
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How can stat major get into bioinformatics?
I'm in my first semester of phd in information science and
I want to work with bioinformatics professors.
As a stat major, what should I prepare for before contacting some of them?
I thought about ...
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Slightly different sequences returned by BLASTP
Probably this is very trivial but I am self-learning bioinformatics and I don't know who to ask for this kind of stuff. Also, apparently it is really hard to find information on general topics like ...
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Is it OK to use predicted protein sequences from RefSeq for protein sequence alignment?
I'm doing a project, and my goal is to do alignments of a particular gene product to see if there is any conservation of secondary structures across different species.
So far, I have found a few from ...
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How to customize the output of my BLASTP output form
I'm trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with ...
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RNA-Seq: Is it conventional to use a threshold RPKM value to determine if a gene of interest is expressed in a sample?
I am interested in finding out at what stages of development a gene of interest is expressed in the human brain. I am using the Developmental Transcriptome tool from the Allen Brain Atlas to find this ...
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