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Questions tagged [bioinformatics]

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

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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 ...
Mikhail Gaichenkov's user avatar
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1 answer
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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 ...
Ivan Spirandelli's user avatar
2 votes
1 answer
54 views

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 ...
aquaporin's user avatar
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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 ...
KGee's user avatar
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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 ...
TheEnvironmentalist's user avatar
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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 ...
User122995767's user avatar
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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 ...
Loki123's user avatar
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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 ...
user135580's user avatar
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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, ...
biohacker's user avatar
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2 votes
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131 views

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, ...
Hannah Lye's user avatar
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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 ...
Shreyash Yadav's user avatar
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1 answer
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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 ...
Wissem Boujlida's user avatar
1 vote
1 answer
86 views

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? ...
Shiran Yuan's user avatar
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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, ...
Maximilian Press's user avatar
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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, ...
Vegetable New Man's user avatar
1 vote
1 answer
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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 ...
Hieronimus Adiyoga's user avatar
1 vote
1 answer
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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 ...
algebroo's user avatar
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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)}{\...
algebroo's user avatar
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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-...
Assa Yeroslaviz's user avatar
3 votes
1 answer
426 views

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 ...
HungryMolecule's user avatar
2 votes
1 answer
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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-...
Fan Yang's user avatar
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1 answer
55 views

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 ...
Abelaer's user avatar
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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<...
gc5's user avatar
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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 ...
user996159's user avatar
4 votes
2 answers
68 views

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 ...
Santiago Bosch's user avatar
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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 ...
Mehad's user avatar
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1 answer
205 views

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 ...
Krellex's user avatar
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4 answers
226 views

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 ...
Ramil's user avatar
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7 votes
1 answer
117 views

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 ...
Jeff's user avatar
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1 answer
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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 ...
Till Hoffmann's user avatar
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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 ...
david1201's user avatar
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26 views

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 ...
Tasneem Qaqorh's user avatar
0 votes
1 answer
136 views

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 ...
Raz's user avatar
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3 votes
1 answer
1k views

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. ...
NoBio's user avatar
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3 votes
2 answers
100 views

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 ...
stevec's user avatar
  • 217
0 votes
1 answer
144 views

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-...
honhon's user avatar
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2 votes
1 answer
93 views

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 ...
subhacom's user avatar
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0 votes
1 answer
112 views

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 ...
070701's user avatar
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0 votes
1 answer
72 views

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 ...
RDGuida's user avatar
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0 answers
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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 ...
help needed's user avatar
0 votes
1 answer
233 views

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 ...
Yuri Rolimus's user avatar
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0 answers
112 views

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 ...
ceno980's user avatar
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2 votes
0 answers
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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 ...
ceno980's user avatar
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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 ...
a4xrbj1's user avatar
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2 votes
0 answers
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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 ...
yters's user avatar
  • 285
0 votes
1 answer
975 views

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. ...
user avatar
2 votes
0 answers
67 views

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 ...
xavayey244's user avatar
1 vote
1 answer
547 views

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 ...
DDS's user avatar
  • 19
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 ...
Manuela's user avatar
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