Questions tagged [bioinformatics]

The science of collecting and analyzing complex biological data such as genetic codes using informatics.

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1answer
252 views

Which are the best programs to analyze circular RNA?

Hello I'm just started with bioinformatics and I would like to know which programs are best for the task of finding circRNA (circular RNA) in sequences of tissues and different cellular types. I have ...
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1answer
896 views

Why do membrane proteins at lower temperatures contain more alpha helices than beta sheets?

Why do organisms found at low temperatures have membrane proteins with a higher percentage of alpha helices compare to beta sheets?
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2answers
301 views

Is setting high mismatch and gap penalties sufficient to distinguish perfectly mapping reads?

I have a fat pile of 125bp whole genome shotgun reads that have undergone quality control, and I would like to pull out just those reads that do not map perfectly to the genome. When I set extremely ...
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1answer
48 views

How can I list genes present on a given series of bands?

My question is related to this one. My interest relate to this deletion: del(7)(q11q36)[12] as defined by ISCN. I would like to access a list of the genes found on the bands 11 to 36 of the 7th ...
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0answers
514 views

How to calculate the Position Weight Matrix score?

Can anyone explain me how to calculate the Position Weight Matrix score? I know the formula, but I don't understand it. I have a table with the frequences of nucleotides, and a table with the PWM ...
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1answer
822 views

What does “local folding” means in secondary structure?

I'm new to biology field, so I'm learning all kinds of biochemistry knowledge for a bioinformatics project. I've found a few definitions of secondary structure online. For example, I found this brief ...
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2answers
233 views

Actual determination of the DNA sequence in the shotgun approach?

I'm studying bioinformatics and I'm confused by shotgun sequencing. In Sanger sequencing we break up the DNA and use ddNTPs in order to determine the exact position of each neucleotide. How exactly ...
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0answers
17 views

Plasmid harbouring subunit S of type I R/M system

We have an assembly of a genome of a Lactobacillus species. The genome also contains a 7.5kb plasmid. Aside from the "usual plasmid genes" the plasmid contains: - toxin/antitoxin system - Subunit S ...
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1answer
799 views

Meaning of ‘NC number’ associated with a gene?‘

Genes in listings etc. often have a number of the type NC_000012.12 associated with them. How should this be interpreted?
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38 views

Are VCF headers supposed to change over time?

VCF headers describing the content of the INFO field are supposed to give additional information about a variant. Example. A VCF file can be annotated against ...
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0answers
103 views

Use of pipe character in VCF info field

While annotating my VCF file with ClinVar, I noted the following value for the CLNSIG field (i.e., clinical significance): ...
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1answer
79 views

What is Genome wide analysis and Locus specific analysis

I am reading some articles on genetic variations and I see there are two types of analysis one is genome wide genetic variation analysis and second one is locus specific genetic variation analysis. I ...
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1answer
5k views

Why should we use the NA12878 dataset for benchmarking?

As far as I understand, the human genome sample called NA12878 provides high confidence variants for a human sample. It is being used as a benchmark for many genomic research projects. Q: Why exactly ...
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2answers
339 views

What's cosmic VCF?

The popular MuTect variant tool: http://archive.broadinstitute.org/cancer/cga/mutect_run has the following VCF option: --cosmic < comic.vcf > Q: What is this cosmic VCF file? What's the ...
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33 views

Blastx: from gi to description

I have done a blastx and use the outfmt 6 option, because I want to work in the tables format. When I do this I get subject ids of the type sp|Q7XJS0|ASHR1_ARATH, sp|Q39547|CUCM1_CUCME, et cetera....
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263 views

Example of code with pypgen (python)

I have a VCF file and wish to calculate a few indices of population divergence over a sliding window. I consider using pypgen but the documentation is currently very limited. Can you please give me ...
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1answer
78 views

What is the secondary structure distribution per AA in the Human proteome?

If one would classify each amino acid to either be in a Coil, Beta strand or Alpha helix what would be the distribution of these classes in the human proteome? Is it 33%-33%-33% or is it biased? If ...
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1answer
847 views

Why not replace the human genome with it's decoy genome version?

https://www.biostars.org/p/73100/ http://www.cureffi.org/2013/02/01/the-decoy-genome/ The decoy genome is an improved human genome from the regular reference. It's faster for mapping and it reduces ...
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126 views

Rosetta - What score does RosettaDock use for I_sc?

I want to get a score using Rosetta for how well a protein binds to a ligand. I understand RosettaDock has a score called I_sc which will give me a number to indicate that. I found documentation in ...
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1answer
122 views

correction of read counts for spikes

I have 4 RNA-seq samples (1st is control and the other 3 are treatments) and 5 spikes. I used different concentrations for 5 spikes but over different samples, I used similar concentration. for ...
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0answers
61 views

Annotation for non-model organism [closed]

I want to annotate data while analyzing transcritpome data using DESeq2 , usually Biomart R-package (https://www.bioconductor.org/packages/release/bioc/html/biomaRt.html) does the needful , but for ...
4
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1answer
76 views

Subset of Protein Crystal Structures (from PDB)

Is there a well-accepted subset of the Protein Data Bank set of protein structures that: Has only "high quality" structures (may be differing metrics of this; e.g. resolution, size, or structural ...
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1answer
145 views

Which DNA sequence will have higher melting temperature: CCCCCC… or GCGCGC…?

I tried this service to calculate temperatures. The nearest neighbour method consistently gives larger results for sequences like GCGCGC over sequences like ...
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1answer
1k views

Confused about the calculation of BLOSUM matrix

I am trying to understand how the BLOSUM matrix is calculated. I found a very nice tutorial here: http://www.cs.columbia.edu/4761/assignments/assignment1/reference1.pdf Also i read through the ...
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1answer
218 views

How can I get the coding region from gene sequences?

So, I have a file with 600+ sequences of a gene, each one from a different population. This file was obtained after blasting the chromosome sequences against the gene sequence. However, I need the ...
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0answers
153 views

VCF files - examples for haploid organisms

I am trying to self-learn some aspects of bioinformatics (coming from a stats background), and i am trying to find / download some VCF files for haploid organisms as an input to some statistical ...
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0answers
47 views

phylogenetics and substitution ratios for positive selection [closed]

So very new to phylogenetics!. I've been scrambling and reading so much to get this done!!. I would like to see if one or more of the sequences I have (from a gene family) are under positive ...
3
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2answers
2k views

How can I evaluate the hydrophobicity and/or surface charge of a protein?

How should I evaluate protein surfaces in terms of hydrophobicity and surface charge properties of the surface. Particularly I am looking to compare hydrophobic patches or surface charge between two ...
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0answers
46 views

How to annotate the SwitchGear gene models?

According to this page(http://switchgeargenomics.com/wp-content/uploads/2009/02/switchdb_technote1.pdf), the SwitchGear gene models can be annotated by the NCBI annotation associated with Refseq ...
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1answer
213 views

Example of well understood/modeled biological mechanism

I am working on modeling psychiatric disorders, where multivariate time series data - which I think is necessary to do any interesting modeling - is only broadly available recently, due to the ...
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1answer
121 views

Why is it desirable to couple chemical production to growth?

I have the following question in systems biology: a) Draw a graph showing the relationship of growth (Vbio) and Vefni for the system here. (Let the horizontal axis represent Vbio and the vertical axis ...
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1answer
292 views

What is “contigs” in Picard's ReorderSAM?

I've used BWA to map my NGS reads against the hg38 genome, and I have a BAM file. I'm not doing genome assembly, and my reference genome file has the human chromosomes. Thus, I shouldn't have "contigs"...
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1answer
218 views

How to write a stoichiometric matrix for a part of the Pentose phosphate pathway

maybe this is more bioengineering than biology but I didn't find any such group. So I got the following photo: And I was asked to do the following for the network inside the red area. 1) Write the ...
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1answer
298 views

Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?

I have a data set of de novo assembled RNA-seq datasets across different sample types. When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. ...
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0answers
388 views

what is the meaning of the genotype values in each snp

I understand that snp is a single base variation. For example, if person 1 has the sequence in DNA , AAGCCTA the second has AAGCTTA, then the allels are C,T. My question is what is the meaning of 0,...
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0answers
498 views

What's the best wat to combine biological replicates in qPCR gene expression analysis? (2^(-∆∆Ct) method; one-way anova, turkey's test)

I am measuring the levels of gene x after transfection of cells with a plasmid and I want to compare them to the levels in mock-transfected cells. I did three different transfection experiments, in ...
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2answers
73 views

Analysis over single chromosome data

I have no expertise in biology, I'm a data scientist, and I would like to know if it makes sense, from the biological point of view, to analyze data (SNP data) coming from a single chromosome, and not ...
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1answer
162 views

What is the most-stable gene identifier?

I've struggled in the past with designing data(bases) around gene-identifiers that evolve over time. For example, UniProt and Ensembl change their identifiers for certain proteins/genes and the IDs ...
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0answers
400 views

Minor Allele Frequency (MAF) higher than 0.5? [closed]

I have a set of data in PLINK format (*.bed, *.bim and *.fam files). There are around 2000 individuals in my dataset. I used PLINK to calculate allele frequencies in the population: ...
2
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1answer
57 views

Organism-specific Kegg Pathway: Must all boxes be high-lighted/present for a reaction to occur?

I'm new to using Kegg and not sure how to interpret the position of the pathway enzymes in the pathway that I'm looking at. More specifically: If all boxes (of KOs) must be present/colored green or ...
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2answers
154 views

Topic in bioinformatics [closed]

I am looking for a presentation topic in bioinformatics. I haven't occupied with this field yet, but I find it really interesting. It would be nice if the topic would include an algorithm. What ...
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1answer
60 views

Which algorithm to find the evolutionary relation of 5 sequences?

After Multiple Sequence Alignment (MSA), data sets are produced on which models of evolution are used. I've seen in books that if there is strong similarity between the sequences then Maximum ...
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2answers
839 views

Books on machine learning applications in Biology

I have recently engaged with a collaboration, which requires me to construct, then train an unsupervised artificial neural network (ANN). However, I have only a very coarse understanding of what ...
1
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1answer
811 views

Reading annotations from a plasmid map

Can anyone explain why inside plasmid mapping software the annotations are layered under each other, I am confused as to why there are essentially two layers within the map, for example in the image ...
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4answers
155 views

Is there a list with common mistakes in database entries?

I am a university student at the department of Biology. As part of my assignment for the subject Bioinformatics, I was asked to refer to common mistakes in biological database (e.g. Uniprot). For ...
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1answer
64 views

Does a software exist to automatically design antibodies that target a given protein or antigen?

I'm looking for software to automatically design antibodies that target a given protein or antigen.
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2answers
89 views

Difference between imputing and typing in GWAS studies?

In genome-wide association studies (GWAS), what is the difference between imputing and typing? Are they the same?
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1answer
566 views

How to find the location of a gene, starting with the gene name and the DNA sequence of nucleotides? [closed]

I'm not a professional biologist, I'm just trying to analyze some actual data. Where should I look up the location of a gene and nucleotides it consist of? How can I find it in DNA? Is there an ...
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1answer
987 views

Whole Genome Sequencing vs Whole Exome Sequencing

I am working on a project where I want to discover causative genes for a certain disease I may have. I was wondering whether to get WGS or WES to perform this experiment:- I am looking at SNP's and ...
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1answer
126 views

Tools that take a kinship matrix for phylogenetic decorrelation

I have plant genotypes that have been classified as Invasive, Wild or Domestic. I am trying ...

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