Questions tagged [bioinformatics]

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

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Construct phylogeny from a Fasta file [migrated]

I have a set 189 sequences in a fasta file. I like to get the phylogenetic tree in newick format. I was using earlier https://ngphylogeny.fr/. Unfortunately now it is not working due to some bugs. ...
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Could someone please help me understand the outputs for HapFlk [migrated]

Could someone please explain the output file for HapFlk? My input file was a ped file which has three different populations. Two with same number of snps by imputation and third one is an outgroup ...
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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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2 votes
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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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What is the fastest way to find all 23-mers in the human genome (GRCh38) that end with NGG?

According to this paper, there are 0.68 billion such sequences. The authors have mentioned that the data was collected from ENCODE. But I could not find any sequence download link on that site. So far,...
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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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7 votes
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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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1 answer
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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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1 answer
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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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2 votes
1 answer
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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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2 votes
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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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1 answer
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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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Is there a reference brain sample for the RNA-Seq data in the Developmental Transcriptome tool from the Allen Brain Atlas?

I am using the Developmental Transcriptome tool from the Allen Brain Atlas to determine at what stages of development a specific gene is expressed in the human brain. I have read the official ...
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Is there a newer/better book than Genome-Scale Algorithm Design available? It's from 2015

I'm considering buying the book "Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing" by Veli Mäkinnen and others. However, as this book was ...
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What reference genome was used to bootstrap the human genome?

As I understand it, when we map a genome, the process is much more complicated than say copying text out of a book. The genetic sequence cannot be copied from a genetic sample in a single pass, so ...
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What is a downstream target?

For example, in a systems biology analysis, what is a "downstream target" and why are these significant in pathway analyses? I have looked for answers on Google, DuckDuckGo, Wikipedia, etc. ...
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How to make Needleman-Wunch algorithm work if I restrict the number of gaps?

For example, I have two sequences (one is longer or equal to another) and I want to make a global alignment between them, but I only want to generate gaps in the shorter sequence. I see that the ...
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2 votes
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Difference between heritability on the scale of liability versus the scale of observation

I was reading a paper on disease heritability ("Estimating Missing Heritability for Disease from Genome-wide Association Studies") and it struck me that I don't have a great understanding of ...
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1 vote
1 answer
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The Portion of the Earth's Biomass Attributable to Ants [duplicate]

An exterminator came to the house today (bad ant problem). He claimed that 20% of the earth's biomass is comprised of ants. I was surprised by this statement. I figured that I would post the question ...
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1 vote
1 answer
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What is sigma factor PvdS?

I am using MEME suite tool for de novo motif discovery and when I use TomTom to compare my motifs with known motif database, I find that my genes could potentially be upregulated or downregulated by ...
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2 votes
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What's the process for determining whether a GC -> AT conversion in bisulfite sequencing is due to degradation?

I'm working on an ancient DNA project (humans) examining the methylation patterns for a single nuclear gene on chromosome 5. I understand the protocols of bisulfite sequencing, and in general how the ...
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What are the prospects in synthetic biology, especially in the introduction of biological computers? [closed]

One of the interesting areas of synthetic biology is the so-called biological computers. A biological computer refers to an engineered biological system that can perform computer-like operations. I ...
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1 answer
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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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1 vote
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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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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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1 answer
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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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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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1 answer
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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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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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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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3 votes
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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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1 vote
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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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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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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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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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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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1 answer
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How to identify an unknown species from its genome sequence [closed]

I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to ...
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2 votes
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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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