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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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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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28 views

How to interpret these mutations obtained from Annovar output file?

Need help in interpreting the following. What does each mutation represent? E115Rfs*24 - If it means that it is a frameshift of 24 nucleotides, then why is it represented as E115Rfs*24 and not as ...
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25 views

For sequence alignment , why isBLAST used for global alignment even though it is based on local alignment approach?

For sequence alignment , why isBLAST used for global alignment even though it is based on local alignment approach?
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9 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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16 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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24 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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22 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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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
31 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
41 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
23 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 ...
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52 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 ...
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1answer
45 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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26 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
20 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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50 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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37 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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103 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
36 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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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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39 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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27 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
54 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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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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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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45 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 ...
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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
30 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 ...
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1answer
60 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
36 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
79 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 ...
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3answers
156 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
27 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 *...
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2answers
55 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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614 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
29 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 ...
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2answers
241 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
40 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
50 views

identification of differentially expressed genes in RNA-seq analysis [closed]

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
53 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
56 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 ...
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1answer
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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 ...