Questions tagged [bioinformatics]
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
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questions
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semantic similarity measurement for cell line ontologies
I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies.
The problem I have is that I have found a Python library called Fastsemsim, but it ...
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0answers
4 views
Differences in webtool and standalone Clustal Omega Percent Identity Matrix [migrated]
I'm trying to align sequences using MUSCLE in my own computer. To compute Percent Identity Matrix I'm trying to use Clustal2.1 like it's done in https://www.ebi.ac.uk/Tools/msa/muscle/. Even though I'...
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1answer
37 views
Proteomics data Vs Transcriptomics data?
I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
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1answer
19 views
Protein structure prediction using PSSM? Or not?
I have been studying protein structure prediction algorithms. A lot of recent work uses something called the PSSM, the position-specific scoring matrix.
I think that what a PSSM does is to build a 2-...
2
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1answer
68 views
How to integrate transcriptomics data with kinetic metabolic models?
I have created a convenience kinetics† model. Now, I want to integrate the transcriptomics data with my convenience kinetics model for altering/weighing the kinetic parameter values. I have ...
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11 views
How to find essential genes by differential expression from TCGA 3rd level CNV data?
I have two types of data one have normal patients copy number variation (CNV) data and another have tumor patients CNV data. In each file there are three columns one contain patient ID, second ...
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1answer
37 views
What does “count in gene set” mean?
I am trying to understand the analysis generated by STRING.
In analysis for biological processes table, there is a column titled "count in gene set." This gives a value for example "68 of 498".
What ...
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23 views
Can GENESIS simulation software be adapted to other types of tissues?
GENESIS simulation software http://genesis-sim.org/ is designed for neurobiological systems and it is able to inculude in the simulation the different resolution levels - starting from the molecular ...
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1answer
36 views
What are names of the colon delimited fields in this FASTA header?
The human chromosome DNA data in Ensembl release 96, here is in FASTA format.
Reading the Wikipedia article on the FASTA format, I understand the first line, prefixed with ...
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3answers
82 views
What is a sequencing artifact?
I'm rather new to bioinformatics, so this might be a rather basic question, but what are sequencing artifacts, in the context of variant calling?
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1answer
13 views
Where to download confier (pine) or A. thaliana annotated reference RNA transcriptomes in full .gbk (GeneBank) format?
Where to download confier (pine) or A. thaliana annotated reference RNA transcriptomes in full .gbk (GeneBank) format?
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38 views
Which database has the ready made 16S rRNA Multiple Sequence Alignment File that I can download directly from?
In my case, I need the ready made 16S rRNA Multiple Sequence Alignment File for E.coli and use it to generate the phylogenetic tree file in Newick format. I've tried using the one from utexas website, ...
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27 views
conversion of distance matrices to pdb/coordinates
I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues ...
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1answer
21 views
How to create a phylogenetic tree (using Maximum Likelihood method) in newick format for a Multiple Sequence Alignment file in FASTA format?
The file size is really big (26.7 MB). So, I am unable to use the online web tools, as they cannot handle such large input data.
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1answer
32 views
How to search for a DNA sequence in a genome on ENA (European Nucleotide Archive)?
I have to do a search for small DNA sequences in the genome of an organism in ENA. I have the accession number and project id. However, I can't download the whole genome because of the download size ...
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16 views
Where can I find and download HMMTOP training set?
I would like to perform redundancy reduction for my test set for membrane topology prediction. I checked the 1998 paper and website of the HMMTOP server but haven't found any download links for the ...
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1answer
26 views
Why do chain identifiers in PDB have no standard starting chain id type?
At first I assumed that PDB chain identifiers are just uppercase letters (A, B, C,..) but found out there are protein chain ids that are numbers (0-9) and lowercase letters as well.
For example,
...
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1answer
28 views
What are primary reasons for the failure to localise/anchor sequences in genome assemblies?
My question concerns the incorporation of individual sequence reads into chromosomes during gene sequencing projects, especially those with larger genomes such as Drosophila melanogaster or Homo ...
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1answer
33 views
Are phylogenetic tree construction algorithms any different than general clustering algorithms?
I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it ...
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1answer
45 views
How to download different kinds of data from NCBI eutils?
I have been researching NCBI eutils and wish to get some 'big data' from it. I know that I can construct queries to query one of (I think) 8 databases, like this:
...
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1answer
24 views
16S rRNA and 5S rRNA datasets
I need 16S rRNA and 5S rRNA (Gammaproteobacteria - E.coli) Secondary structure files in ct format.
I tried looking for them in different RNA databases, could not find one. Can someone tell me where ...
2
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1answer
62 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
48 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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29 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
22 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
115 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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32 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
41 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’...
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1answer
107 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
41 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
26 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
52 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
29 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 ...
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1answer
43 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 ...
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2answers
60 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
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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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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 ...
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2answers
133 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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15 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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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
31 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
47 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
62 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
41 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 ...
2
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0answers
80 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
160 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
26 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
28 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
43 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 *...
