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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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38 views

Where are there analyzable signed directed network datasets?

I'm looking for biological datasets with specific properties that are available for me to analyze. Informally put, I have a hammer and I am looking for a nail. That is to say, I have an algorithm and ...
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1answer
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Relationship of RNA-binding proteins to peptidyl-prolyl cis-trans isomerase

I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?
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46 views

Extract mutations from fasta sequences

I have a large amount of protein sequences in the .fasta format and I would like to extract only the amino acid mutations from these sequences, so that, in the end, I want to have a list that looks ...
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Which molecular dynamic simulation software is more applicable for protein and large-area surface interaction simulation? And how to run it?

I am trying to do the molecular dynamic simulation for protein-surface interaction, the surface (like cellulose or PET) is a film-like or crystalline material with large surface area, I had tried ...
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Where can I find the genome of the L-strain coronavirus and the S-strain coronavirus?

I read an interesting article about two strains of the coronavirus: https://www.newscientist.com/article/2236544-coronavirus-are-there-two-strains-and-is-one-more-deadly/ I would like to know how the ...
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Can non-directional and bi-directional features be described in genbank format?

I'm just wondering if there is a standard way within genbank files (.gb) to specify that a feature is non-directional or bi-directional. I don't see any info on the https://www.ncbi.nlm.nih.gov/...
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27 views

In the notch signaling pathway, what is Fringe activating?

Take a look at the notch signaling pathway in human from KEGG : https://www.genome.jp/kegg-bin/show_pathway?hsa04330 I want to know what is Fringe activating. It is not pointing to another gene or ...
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Outlining cell edges of an epithelium

Is there any free software (for Windows, preferably) to detect cell edges in pictures of an epithelium, for example? I know Packing Analyzer does this, any other suggestions? Ideally, I would like ...
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1answer
72 views

How to do research in bioinformatics without wet lab experiments?

I graduated in physics from Bangladesh and keen to work in the field of biology. Like, systems biology, computational biology, bioinformatics or systems medicine. I have not produced any research work ...
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Why use log odds and not probability to construct substitution matrices?

I'm studying "Understanding Bioinformatics" by Marketa Zvelebil. I came to know that substitution matrices (PAM, BLOSUM etc) use log odds and my immediate thought was why not use probabilities. ...
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Mendelian randomisation and covariates

I am using a mendelian randomisation (MR) approach to determine whether there is a causal effect of an exposure X on the outcome Y. To do so, I run a genome-wide association study (GWAS) of the ...
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Trying to understand PAM matrices

If I have several PAM matrices all computed using different evolutionary distances, and I compute the score between two amino acid sequences, is the max score I get using any one PAM matrix the most ...
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1answer
20 views

Is there a difference between splice-site mutations, and non-stop mutations

I'm working on a bioinformatics project where a lot of the biology I've had to learn from scratch. From my current understanding, a non-stop mutation alters a stop codon such that the transcription ...
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1answer
40 views

What is the technical term for when a clade on a phylogenetic tree does not have an extended branch? (see image)

As we see with ZCA2, ECA2 & XCA2 these branches are compressed and do not extend as TCA does. Is there a technical term for this and what usually causes it?
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How many atoms has the smallest known bacterium? [closed]

Background thoughts before this question: is it feasible to simulate a complete bacterium, atom by atom, in a computer simulation? On modern systems, either in an upcoming exascale computer? In ...
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What tool can I use to align multiple protein sequences to one reference sequence?

I have a protein of interest which is ~300 amino acids in length. I also have around 40 short sequences (all 9 amino acids in length); these are all very different from each other. I would like to ...
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Can two proteins activate/inhibit the same gene at the same time?

Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right? So if one protein has already inhibited that gene before ...
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Where to find a list of genes coding for protein in human

I have raw read counts extracted by htseq from STAR alignment I have both data with both Ensembl IDs and gene symbols, but I need only a latest list of protein coding genes in human; I googled but I ...
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59 views

Help on selecting 2 tests - unsure if they are paired or non-paired statistical test

I have data that measures the temperature of flowers and leaves on different plant species. These are the comparisons I am trying to make: Comparing the flower and leaf of the same plant at the same ...
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What are the methods for detecting anagenetic versus cladogenetic change?

I'm new to the study of phylogenetics and am wondering if there are ways of identifying evolutionary changes that associate with cladogenetic events versus those that arise via anagenesis.
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Is there a system biology approach to compare pathways or famillies of proteins from an evolutionary point of view for the same organism?

I would be interested to know if there is a method/analysis or a set of methods to compare two groups of pathways or families of proteins. I would specifically be interested by a system biology ...
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54 views

Where can I obtain the sequence of the E. coli ribosomal RNA precursor?

I have found separate sequences for 16S rRNA (from the small subunit) and 23S rRNA and 5S rRNA (from the large subunit). I need the full precursor rRNA sequence, which I cannot find. However the ...
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1answer
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How accurate are Illumina microarray chips for genotyping?

What is the error rate for these machines in genotyping (like for 23&me)? What is the chance of a false positive or false negative?
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How to reduce the number of sequences in a Multiple Sequence Alignment?

I have a Multiple Sequence Alignment, where there are around 5000 sequences. There also exists many sequences where, there are so much of non-sequenced regions (for instance, AU----CGGGCA--NNNNNNNNNN)....
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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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1answer
47 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
39 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-...
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1answer
79 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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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
101 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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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
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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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575 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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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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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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44 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
33 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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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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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
59 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
31 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
36 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
63 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
34 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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1answer
83 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
84 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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1answer
31 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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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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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
66 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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