Questions tagged [bioinformatics]

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

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1answer
243 views

Longest transcripts without isoforms

Does anyone know what genes produce the longest mRNAs? I am planning a project on synthetic introns and want to use stuffer fragments to vary intron size. Obviously they must not contain any splicing ...
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Basic molecular biology of nucleic acids book for a mathematician studying DNA and RNA formally?

I am a mathematician studying DNA and RNA language from the perspective of Formal Language Theory. Note that I am aware of these posts: best book for a comprehensive introduction to biology for a ...
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1answer
98 views

Webtool to design guide RNA (gRNA) for use with CRISPR-AsCpf1?

My goals are to use a free webtool to: Identify guide RNAs (direct-repeat sequence followed by the targeting sequence) appropriate for use with AsCpf1 in order to target a specific segment of genomic ...
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1answer
51 views

Do mutations in one bacterial strain have the same effect in other strains within the same species?

I would assume so, since they are the same species after all. I am asking this because I am doing a bioinformatics project for school and I cannot find any protein mutations for the specific bacterial ...
2
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1answer
36 views

What would be the difference if I use the Web server instead of dedicated server for protein modeling and docking?

We know that software tools like I-tasser etc have a web server and a standalone option too. Is there any difference to protein C-scores or efficiency or accuracy if you do it on standalone instead of ...
2
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1answer
105 views

How do we know which Eulerian path corresponds to the DNA sequence?

Bioinformatics textbooks explain one method to reconstruct the whole DNA sequence from multiple reads. The method builds a graph and finds a Eulerian path in it. The Eulerian path corresponds to a DNA ...
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2answers
74 views

Predict if a given protein is recognized by antibodies

Assume that i have a 3d-protein structure in a PDB file on a computer. Is there any bioinformatic method to predict if that protein is recognized by all known antibodies of human and cause an immune ...
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0answers
30 views

Predict if a given protein can pass through the intestine

Assume that i have a 3d-protein structure in a PDB file on a computer. Is there any bioinformatic method to predict if that protein can pass through the intestine or not?
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501 views

Understanding PAM and BLOSUM matrices

This question might be silly but I need some clarification. I'm slightly confused about if there are multiple PAM and BLOSUM matrices? Is there a different matrix for each sequence? My ...
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1answer
352 views

What is the best alignment definition for the Multiple Sequence Alignment (MSA) problem?

For simplicity, suppose that I am penalising mismatches and gaps with -1 and adding a score +100 for each match. Does the optimum alignment of the three DNA sequences ...
3
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1answer
459 views

What is meant by “genes at the trunk of the evolutionary tree”?

Recently I went through a paper about hepatocellular carcinoma in which they talked about trunk genes (p. 26, second paragraph): Branching tumor evolution complicates efforts to implement ...
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55 views

Can someone explain what exactly each score of the BLOSUM62 matrix means? [duplicate]

The descriptions that I've found say it's the log odds ratio (observed/expected) where expected is the assumption that there is no correlation between amino acids. I'm slightly confused as to what ...
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0answers
63 views

How to evaluate broad-sense heritability of microbiome associated plant genotypes in R

I have a data containing 196 accessions of A. thaliana from which I studied leaf bacterial and fungal community and, therefore, sequenced and found several OTUs. Now, I want to evaluate broad-sense ...
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2answers
720 views

How to combine gene set enrichment analysis with hierarchical clustering?

I would like to find out how to combine gene set enrichment analysis with hierarchical clustering. The motivation for this combination is that potentially too many gene-set symbols for leukemia may ...
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1answer
256 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
1k 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
373 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 ...
2
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1answer
50 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
543 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
1k 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
241 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
20 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
1k 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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0answers
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
114 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
80 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
361 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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35 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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267 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
914 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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1answer
180 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 ...
3
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1answer
131 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
66 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
82 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
266 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 ...
2
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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
221 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
170 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 ...
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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
220 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
142 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 ...
2
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1answer
307 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
270 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
311 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
392 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
552 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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