Questions tagged [bioinformatics]

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

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3answers
81 views

Do DNA footprints vanish in generations?

Consider humans (or really any creature with sufficiently complex set of genes). If person $A_0$ has an offspring, say $A_1$, we can without a doubt find markers in $A_1$ that we can definitely say ...
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0answers
227 views

How to correlate survival probability to gene expression profile?

I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how ...
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1answer
30 views

Query regarding calculation of survival analysis

According to this tutorial, for table to find the survival estimates, the square root of the 6th column is multiplied with the 4th column, which is Survival probability. The value that should come for ...
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1answer
447 views

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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25 views

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 ...
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1answer
440 views

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 ...
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3answers
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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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2answers
159 views

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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2answers
45 views

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 ...
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1answer
479 views

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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0answers
34 views

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 ...
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2answers
170 views

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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0answers
331 views

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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1answer
196 views

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 ...
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1answer
210 views

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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0answers
81 views

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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3answers
255 views

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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0answers
32 views

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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2answers
944 views

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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22 views

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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1answer
115 views

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 ...
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1answer
53 views

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 ...
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2answers
135 views

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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2answers
210 views

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 ...
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0answers
82 views

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 ...
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1answer
103 views

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 ...
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2answers
75 views

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 ...
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1answer
101 views

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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1answer
110 views

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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0answers
64 views

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 ...
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0answers
127 views

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 ...
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2answers
84 views

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 ...
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1answer
62 views

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 ...
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1answer
192 views

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). ...
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2answers
87 views

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, ...
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1answer
259 views

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 ...
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2answers
15k views

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?
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1answer
106 views

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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1answer
119 views

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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1answer
235 views

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 ...
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0answers
76 views

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 ...
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1answer
93 views

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 ...
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1answer
49 views

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 ...
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1answer
36 views

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 ...
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1answer
104 views

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 ...
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2answers
73 views

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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0answers
30 views

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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0answers
479 views

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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1answer
336 views

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 ...

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