Questions tagged [bioinformatics]
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
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1answer
35 views
How many palindromic sequences in human genome?
I'm writing an article on palindromes (the words) and I wanted to mention the existence of palindromic gene sequences. Roughly how many palindromes exist in the human genome? I understand the number ...
2
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1answer
32 views
Meaning of PAM matrix values
If PAM-1 matrix refers to time or evolutionary event for 1% change in amino acid sequence of a protein then how come there is PAM250? shouldn't PAM 100 be the highest where the two concerned sequences ...
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0answers
17 views
how do you get a primer for unknown DNA in sanger method? [closed]
how do you get a primer for an unknown dna in sanger method
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19 views
Is there a consensus on the best Machine Learning model for Antimicrobial Resistance (AMR) prediction?
Prediction of bacterial resistance/susceptibility to antimicrobials (from genotypic data) using Machine Learning methods is a problem that has started receiving interest in recent years.
The ...
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1answer
16 views
Is it PSI-BLAST or BLASTP if I use PSI-BLAST for only one iteration
In my case, I used PSI-BLAST in the local BLAST+ to search queries against the self created database. After the first search, I added the searched result to the database and then conducted the ...
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0answers
11 views
PSI-BLAST search result, what can you describe about a protein, especially about their possible functions [on hold]
I looked up this protein on psi blast
MNNLLKIYSDSNDTKLKLVKEGIEEQGICYEILSLKSAYNLDIKKHPFSLAIIIDNKDILIKSINFIKRI
NFNVENISNKYLKEVGLDIGRYIKGFPLKGDW
and I did iteration 3. But I don't know how to describe ...
2
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0answers
28 views
Why do BRAF mutations appear more in skin cutaneous melanoma?
When looking at the tissue expression of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. There is elevated expression in tissues like the Testis and the ...
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0answers
27 views
Frequency of nucleotide sequences of specific length in DNA
How frequently would you find the nucleotide sequence GGATATCCGC (5' to 3' direction) by chance in a DNA molecule?
On average, how many times do you expect to find a specific 20 nucleotide sequence in ...
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1answer
33 views
How many proteins on PDB have unknown function?
I was wondering how many of the files in the Protein Data Bank (PDB) have unknown function. The only paper I can find from an internet search is this one from 2012, which I assume might be outdated. I’...
3
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1answer
98 views
How to interpret this PubChem record of L-Alanine
Using the PUG service from NCBI, I am retrieving 3d structure data for a molecule.
Raw data here.
I am trying to understand this record, specifically for the purpose of rendering in a 3D coordinate ...
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1answer
30 views
From refseq ids to Go term Ids
I have a list of Refseq accession numbers such as :
YP_009448812
YP_009448725
YP_009448701
NP_659591
around 10 000 acc_numbers...
and I'm looking for a tools in ...
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0answers
25 views
How did Smith et al 2004 deal with missing HI [Hemagglutination Inhibition assay] values and HI values <10?
In the scientific paper "Mapping the Antigenic and Genetic Evolution of Influenza Virus's" Supporting Material, Smith et al write about determining antigenic distance Dij. However, I don't understand ...
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2answers
30 views
GEN file format, SNPs and alleles
I have a few questions I can't seem to get a straight answer to, regarding the .gen file format and also biology in general.
The ...
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0answers
25 views
Projects in DNA Computing [closed]
I am physicist and have recently heard about DNA computing. I want to work in this area.
I want your ideas on a "feasible but new project" (maximum time I can put on the project: 6 Months ), I can ...
0
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1answer
42 views
Question regarding when it's a homoplasy in a phylogenetic tree
If you have 2 organisms that both come directly from the same common ancestor on a phylogenetic tree, and that common ancestor does not have trait "x", is it possible for both of its direct ...
2
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2answers
42 views
Meaning of Phred score - probability of base calling error
I learned that Phred quality scores are logarithmically linked to error probabilities. For example, if Phred assigns a quality score of 10 to a base, the chances that this base is called incorrectly ...
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0answers
17 views
Data base or computational tool to help predict if two predicted interacting surface proteins are located on separate cells or on the same cell?
Is there any computational method or database with the help of which one could predict if two interacting cell surface proteins are located on separate cells or are located on the same cell surface?
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0answers
9 views
Is there a measure for degree of reticulation in a phylogenetic network?
When working with phylogenetic networks, how does one talk about reticulate (i.e., web-like) the branches are? Is there a standard measure of this?
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0answers
43 views
Given a list of cell surface genes, is there a computational possibility to predict their interaction partners on the surface of another cell?
After performing differential expression analyses with the Seurat package on my single cell RNA sequencing data from ILC2s of mouse origin, I generated a list of differentially genes. I afterwards ...
3
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2answers
128 views
Does the brain have a clock and can it be sped up?
Before i start, I'm an engineer and have very limited knowledge on biology and neuroscience. My question is, does the brain have a clock like a computer where it has a set processing speed?
Clocks in ...
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0answers
14 views
What software is good for the Y STR data processing?
What software is good for the Y STR data processing? I have Arlequin, Structure, GeneLand and Cervus. What is a better choice for the data processing of haploid Y STR data for the estimation of a ...
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0answers
8 views
What parameters of a blast file are appropriate to detect the real positives
I am analyzing the NGS results. I don't know what parameters of a Blast file I should choose to filter the positives:
...
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1answer
28 views
Amino acid substitutions near the receptor binding site HA protein in type A H3N2 influenza strains?
I have read the scientific paper, "Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution" by Björn F. Koel et al (http://science.sciencemag.org/...
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1answer
45 views
What does it mean by “end effects can be ignored”
I have been reading a book ( Statistics for Biology and Health) and i encountered many of following bold text.
Consider a long DNA sequence of length N, where N is assumed to be
so large that end ...
2
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1answer
55 views
Gene vs Protein homology
I am trying to find homologs for some proteins and I am wondering if it is better to find it by comparing the proteins or the coding genes or either is fine.
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1answer
31 views
Observed to Expected CpG
Observed to Expected CpG is calculated as below :
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence.
I also don't ...
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0answers
78 views
Are evolutionary algorithms calculated in polynomial time? [closed]
How complex are evolutionary algorithms? Also, what is the relationship between variational principles (Lagrangians, minima and maxima,) and evolutionary algorithms? Basically, how hard is it right ...
2
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3answers
118 views
Strand representation in the DNA version of the Genetic Code
A Wikipedia entry entitled DNA Codon Table states that the codons presented in the table are on the ‘sense strand of the DNA’. But what is the purpose of this, if the sense strand doesn’t code for ...
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1answer
25 views
How does one predict how large of an effect on antigenic drift a substitution in the amino acid sequence of a surface protein of influenza has?
I know that some amino acid substitutions are more effective in causing antigenic drift than other substitutions based on their location in the 3d structure of the HA protein (proximity to the ...
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0answers
25 views
Brownian motion : Understanding the output of mvBM function.?
To fit the brownian motion for independent evolution of traits i used below code:
...
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1answer
42 views
GC content of a protein-coding region
I have computer science background and I am trying to understand the equation below.
The average value of the G + C content of a protein-coding region is
given by :
(G+C)= $\sum_{\alpha} (I_\alpha *...
3
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2answers
54 views
Difference between NCBI's /genomes and /1000genomes
Wondering what the difference is in the data hosted here:
ftp://ftp-trace.ncbi.nih.gov/1000genomes
ftp://ftp.ncbi.nih.gov/genomes/
Also (sidenote), would be interested to note what the difference ...
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1answer
311 views
Programming Languages for Bioinformatics [duplicate]
Good day everyone,
I am very much interested in math, biology, and programming; ideally I would like to study bioinformatics and, as such, was wondering what languages are typically used by ...
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1answer
27 views
Can I simulate a previous and next sequence of my fasta files?
I have fasta sequences of a virus protein that had suffered a mutation in 2008 and this mutant had increase it fitness when compared to wild strain (according to literature).I want to simulate if my ...
3
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2answers
150 views
How are cell death like apoptosis and entropy related?
In Perspectives on Statistical Thermodynamics, Yoshitsugu Oono, it is written that
Do not conclude, however, that since the second law is invincible,
information thermodynamics is unimportant. It ...
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1answer
35 views
How to set the phenotype in GWAS analysis?
In the GWAS analysis, my animal sample phenotype is whether an individual dies or survives. And I have every sample death time. How do I set the phenotype in GWAS analysis?
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2answers
40 views
identification of differentially expressed genes in RNA-seq analysis [on hold]
I am using four different packages (viz. EBSeq, DESeq2, edgeR, LPEseq) for identification of differential genes. Now I am confused whose fold change value should I take for further downstream ...
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3answers
50 views
why and how multi allele gets reported during variant calling in vcf?
This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can ...
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1answer
54 views
What do these novel splicing sites mean?
I'm sure that the anwser is obvious for some of you but I just endend my internship where we found novel splice junctions (junctionseq; RNAseq data) (see the attached file) and I have some ...
3
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1answer
30 views
Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?
I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the discussion. The R package 'plotly' enables rendering online-publishable tables ...
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1answer
42 views
How does collaboration on reconstructing metabolic networks work?
I am a researcher in psychology and I am trying to come up with a framework/platform in which psychological phenomena can be studied from a dynamical systems / computational perspective in ...
1
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1answer
91 views
Giga base or Giga byte [closed]
"we reported ~2.66- Gb genome sequence of"
"we generated 191.5 Gb high quality reads"
I am very confused with these two quoted lines and I am not sure about giga byte or giga base pair.
and an ...
3
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2answers
151 views
Can two proteins sharing a few domains be considered homologous?
I wonder when to say two proteins are homolog. In the current example I checked the sequence of these two proteins in pfam and as you see they have some shared domains but all domains are not shared. ...
1
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1answer
47 views
Consensus symbols in multiple sequence alignment [closed]
I was using multAlin for multiple aligning a set of sequences. The output I and came across included the following documentation (English corrected):
Consensus symbols: ! is any of IV $ is any ...
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0answers
33 views
What can I research for thesis on DNA data storage from math? [closed]
I'm a math researcher, I just finished a Master on Error Correcting Codes. I recently saw a presentation on DNA-based data storage that I loved.
I wish to continue my studies on (applied mathematics) ...
3
votes
3answers
81 views
Biological validation of computationally determined gene-gene interaction
How can a computationally determined three-way gene interaction be biologically validated? What kind of assays or tests must be performed using cell/tissue-based and/or mouse models to prove that the ...
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0answers
30 views
How to calculate the Marker Index(MI) for a dominant marker such as RAPD and ISSR?
I am working in the genetic diversity analysis of a plant species and have used RAPD and ISSR markers. After scoring the data in a binary matrix, I am trying to find the marker index of the primers. I ...
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1answer
38 views
Is it possible to re-align of SAM/BAM files?
I am carrying out some metagenomic comparison using whole genome sequencing approach. I would like to filter out reads from my files in a sequential manner, thus I would like to align to a first ...
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0answers
38 views
Use of eigenvalues of Sturm-Liuville operator
I am wondering what would be application in biology where bounds on the Eigenvalues of Sturm-Linville operator would be important?
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0answers
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Is there any data to explore the heterozygosity of the South African lion over the last 18 years?
Background:
I need to find data on the heterozygosity of the south African lion over the last 18 years... and I'm struggling: so far I have found a single data point.
Question:
Where can I find ...
