Questions tagged [bioinformatics]
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
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Could AI be applied to protein folding?
Two years later, there is a follow up question to the one asked here: How do we know if the folding@home project results are right?
Since we are quite sure F@H is working right and following this ...
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Characterising mechanisms responsible for generating structural variants
I have a high-quality set of structural variant breakpoints from tumour/normal WGS data, and I am interested in digging into the various mechanisms that might be involved in each event.
There are ...
2
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1
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How interrelated are computational biology and biophysics? [closed]
I am considering applying to Ph.D. programs, and am not sure what direction to take. I'm hoping you all can help me out.
I have a background in both biology (molecular focus) and physics (condensed ...
2
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Why does sequence of amino acids presented on the Catalytic Site Atlas from a given protein differs from the sequence on the RSCB Protein Data Bank
I wanted to compare the amino acid sequence of enzymes for this project I'm working on and need to compare them at their catalytic site. For that, I went to the Catalitic Site Atlas to get the ...
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2
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Blast databases
I am helping a colleague setup a local blast server. My background is computer science so I apologize if I use incorrect terminology.
Using the NCBI blastn webpage, one of the databases listed is "...
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2
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If we introduce any disease or deadly effect to a large group of living things, will such a group be able to develop a resistance? [closed]
Like for instance, introducing cancer or radiation,
to a large group of insects/animals that can reproduce very quickly,
would it result in the surviving population of these living things to be more ...
0
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1
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Resource for learning analysis of sequence data via QIIME 2
I am trying to study/learn metagenomics through 16s rRNA microbial data and I want to teach myself/review core biology concepts while also learning the QIIME 2 analysis pipeline, as the website ...
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What is the difference between phylogroup and subclade? [closed]
Looking for clarification in terminology, examples would be greatly appreciated!
Not sure how this is off-topic. It is a general question about the difference between biological concepts defined in ...
3
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2
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How to determine the primary Uniprot accession number from a list of accession numbers?
Given a list of UniProt IDs that are linked to an Ensembl ID, is there a way to systematically determine which is the primary accession number with no other information?
According to ExPasy
...
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0
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What is a proper software to do GWAS analysis of tuberculosiis VCFs and phenotype data?
What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association ...
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Alternatives to NCBI BLAST during US government shutdowns?
Many molecular biologists are used to going to NCBI BLAST for quick, hassle-free BLAST searches of their genetic or protein sequences.
However, during the last American government shutdown in 2013, ...
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How much variation in mutation rate in there in the human genome?
In humans, the average mutation rate is estimated to be around $2.5 \cdot 10^{-8}$ (Nachman and Crowell, 2000). Of course this mutation varies from sequence to sequence.
Can you please give some ...
0
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Confirming exon shuffling in a gene
I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, gene sequence, and mRNA (with defined exon/intro ...
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The advantages of using a strand specific cDNA in RNA-Seq?
May I ask what are the advantages of using a strand specific cDNA library in an RNA-seq experiment? as far as I know it can make us able to read the code region but what about other advantages?
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API for gene names by location
Is there any API where I can input chromosome location and it will provide us gene names, for example input chr: 1 location 154714693:154754070 and it will return a list of gene names or ID within ...
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Fisher's Method to melt p-values for CpG sites annotated to the same gene?
I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
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Biological meaning of read length
I have some FASTQ files in two datasets which are sequences from 16Srna region. The first dataset is amplicons form V4 region and the second is V3-V4 region.
However all the reads are 250 nucleotides ...
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What are the chemicals of betel leaves that may react with estrogen?
Im conducting this experiment about pregnancy testers.Im not quite sure what extract method i can use regarding this experiment.any thoughts?? please help me..
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Spatiotemporal patterns in neural networks
It turns out that my work in nonlinear dynamics directly maps to a close variant of the Integrate and Fire model. My model produces spatiotemporal patterns that resemble foam. I have to stress that ...
2
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1
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How should you choose from the various methods of constrained ordination?
I have a bacterial OTU matrix from various sample points and times. So for each sample I have the sequence counts across the various OTUs that they were assigned to.
I also have a corresponding ...
2
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2
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Differential Gene Expression
I have a matrix two gene expression datasets, one from 10 normal individuals and ten from diseased individuals, which are normalised log fold change values--, i.e., already processed.
My question is:...
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2
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What is the best way to calculate the biological diversity of samples from bacterial/viral OTU tables?
I have a few large OTU tables of bacterial and viral datasets. The samples are across different sites and times.
I would like to visualise the community 'diversity' across the times for which I have ...
3
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0
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Should you perform an ordination (such as PCA) of abiotic variables before a Redundancy analysis (RDA)?
I have a dataset of viral 'OTUs' across various sample points from different sites/times.
I also have meta-data collected at these same sample points, for things like temperature and the ...
2
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1
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Phasing haplotypes
I'm new to this area (but not to programming & algorithmics) and I want to help a friend to solve a problem (I don't need source code, I just want to understand the problem itself).
He needs a ...
1
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2
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Analyzing Messy Data Files [closed]
I was writing some code scripts to analyze some plasmodium spp. using this database. However the names assigned to the various epitopes and other items on the list is very very very disorganized. In ...
0
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Open databases for copy number variations similar to TCGA
The Cancer Genome Atlas(TCGA) has open data for copy number variation(CNV) from at least 10k different cancer patients. They offer two types of data, CNV data from tumor and CNV data from normal ...
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Success of computer simulations in biology, new discoveries [closed]
In an interview with Tim Hunt, Hunt makes the following comment:
There are some people nowadays who think you can sort of model everything on a computer. But I'm not one of those. I don't think ...
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0
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Figuring out an honest indicator in intrasexual selection [closed]
In the first picture, the parameter $r$ seems to compare the direction and strength of two variables. In the second picture, $R^2$ seems to describe the variation of proportion of independent and ...
2
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0
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Protein/ligand affinity databases?
Is there any database that contain binding affinities reported in litterature for different proteins and ligands?
I have checked uniprot already and it does not seem to included any binding affinity ...
0
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2
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89
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Why would there be a spike in coverage within a gene in RNA seq data? [closed]
I'm looking at RNA seq data in Geneious for Salmonella typhimurium and I occasionally see a spike in coverage for a sequence of RNA within a gene. Why is there a section of the gene that seems to be ...
1
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1
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Number of elongating RNA polymerases on a gene
I'm interested in knowing how many Pol II molecules are simultaneously transcribing any given gene. There are RNA pol II ChIP-seq (phospho-S5) data for different cells but these come from pooled cell ...
0
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Inheritance of mitochondria [closed]
Imagine an isolated population in which each adult female has a distinct mitochondrial genome. In each generation, every adult female has two children (with a 50% chance of being male or female). ...
2
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2
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Predicting DNA nucleotide bases sequence from fully formed protein
I know there are many algorithms (and a lot of different implementations) that allow predicting the outcome of protein synthesis given a set of nucleotide bases present in the DNA. In other words, ...
6
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1
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Where can I find large datasets of protein-interaction networks?
Where do I find large datasets of protein interaction networks for cancer or alzheimer diseases? So far, I found String but it is does not have enough proteins for my purposes. Are there such ...
13
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2
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How to convert bwa mem output to BAM format without saving SAM file
I want to go straight from bwa mem alignment to BAM format as I don't need the SAM file and it takes up too much space. How do I achieve this?
2
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Copy number regulation & CNV
I have some genes which showed copy number loss between two groups. Now I want to see the copy number regulation of those genes. I really don't know about this concept. Can anyone please tell me ...
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Can qPCR primer with several mismatch works?
I am designing primers for qPCR from conserved regions of a few different fish species.This is because gene sequence for my fish species are yet unavailable in NCBI database.
Is it OK (can the primer ...
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1
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Longest transcripts without isoforms
Does anyone know what genes produce the longest mRNAs? I am planning a project on synthetic introns and want to use stuffer fragments to vary intron size. Obviously they must not contain any splicing ...
2
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Basic molecular biology of nucleic acids book for a mathematician studying DNA and RNA formally?
I am a mathematician studying DNA and RNA language from the perspective of Formal Language Theory.
Note that I am aware of these posts:
best book for a comprehensive introduction to biology for a ...
3
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Webtool to design guide RNA (gRNA) for use with CRISPR-AsCpf1?
My goals are to use a free webtool to:
Identify guide RNAs (direct-repeat sequence followed by the targeting sequence) appropriate for use with AsCpf1 in order to target a specific segment of genomic ...
0
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1
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Do mutations in one bacterial strain have the same effect in other strains within the same species?
I would assume so, since they are the same species after all. I am asking this because I am doing a bioinformatics project for school and I cannot find any protein mutations for the specific bacterial ...
2
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1
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What would be the difference if I use the Web server instead of dedicated server for protein modeling and docking?
We know that software tools like I-tasser etc have a web server and a standalone option too. Is there any difference to protein C-scores or efficiency or accuracy if you do it on standalone instead of ...
2
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1
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How do we know which Eulerian path corresponds to the DNA sequence?
Bioinformatics textbooks explain one method to reconstruct the whole DNA
sequence from multiple reads. The method builds a graph and finds a Eulerian path in it. The Eulerian path corresponds to a DNA ...
2
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2
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Predict if a given protein is recognized by antibodies
Assume that i have a 3d-protein structure in a PDB file on a computer. Is there any bioinformatic method to predict if that protein is recognized by all known antibodies of human and cause an immune ...
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0
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Predict if a given protein can pass through the intestine
Assume that i have a 3d-protein structure in a PDB file on a computer.
Is there any bioinformatic method to predict if that protein can pass through the intestine or not?
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Understanding PAM and BLOSUM matrices
This question might be silly but I need some clarification.
I'm slightly confused about if there are multiple PAM and BLOSUM matrices? Is there a different matrix for each sequence?
My ...
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What is the best alignment definition for the Multiple Sequence Alignment (MSA) problem?
For simplicity, suppose that I am penalising mismatches and gaps with -1 and adding a score +100 for each match.
Does the optimum alignment of the three DNA sequences
...
3
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1
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What is meant by “genes at the trunk of the evolutionary tree”?
Recently I went through a paper about hepatocellular carcinoma in which they talked about trunk genes (p. 26, second paragraph):
Branching tumor evolution complicates efforts to implement
...
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Can someone explain what exactly each score of the BLOSUM62 matrix means? [duplicate]
The descriptions that I've found say it's the log odds ratio (observed/expected) where expected is the assumption that there is no correlation between amino acids.
I'm slightly confused as to what ...
2
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How to evaluate broad-sense heritability of microbiome associated plant genotypes in R
I have a data containing 196 accessions of A. thaliana from which I studied leaf bacterial and fungal community and, therefore, sequenced and found several OTUs. Now, I want to evaluate broad-sense ...