Questions tagged [bioinformatics]
The science of collecting and analyzing complex biological data such as genetic codes using informatics.
890
questions
0
votes
0answers
13 views
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. ...
0
votes
0answers
12 views
How could I match atom orders between a .mol2 and a .pdb? [migrated]
When I was drawing conformation of Autodock result, I noticed that Autodock generated pdbqt from dlg has some structural problem (e.g. Benzene ring missing), and wants to correct this. However I ...
0
votes
0answers
10 views
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 ...
0
votes
0answers
22 views
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 ...
2
votes
1answer
19 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 ...
1
vote
1answer
36 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?
3
votes
1answer
146 views
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 ...
1
vote
3answers
53 views
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 ...
1
vote
0answers
48 views
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 ...
-1
votes
1answer
33 views
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 ...
-1
votes
1answer
58 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 ...
0
votes
0answers
46 views
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.
1
vote
1answer
34 views
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 ...
0
votes
1answer
53 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 ...
1
vote
1answer
42 views
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?
0
votes
0answers
26 views
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)....
0
votes
0answers
16 views
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 ...
0
votes
1answer
45 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 ...
1
vote
1answer
37 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
votes
1answer
77 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 ...
0
votes
0answers
12 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 ...
0
votes
1answer
86 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 ...
0
votes
0answers
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 ...
3
votes
1answer
39 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 ...
2
votes
3answers
375 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?
0
votes
1answer
14 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?
0
votes
0answers
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, ...
0
votes
0answers
39 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 ...
0
votes
1answer
32 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.
0
votes
1answer
37 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 ...
1
vote
0answers
17 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 ...
3
votes
1answer
57 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,
...
0
votes
1answer
30 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 ...
1
vote
1answer
35 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 ...
1
vote
1answer
61 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:
...
1
vote
1answer
33 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
votes
1answer
79 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
votes
1answer
76 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 ...
0
votes
0answers
33 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 ...
0
votes
1answer
29 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 ...
2
votes
0answers
123 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 ...
0
votes
0answers
34 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 ...
1
vote
1answer
62 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
votes
1answer
108 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 ...
1
vote
1answer
55 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 ...
0
votes
0answers
29 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 ...
1
vote
2answers
117 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 ...
1
vote
0answers
36 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
votes
1answer
52 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
votes
2answers
84 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 ...
