The study of genomes, the entire set of genes in an organism.

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Genome and Proteom

Due to the dynamism of protein expression, a genome conducts to different proteomes, but could we say that a proteome comes from different genomes?
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How much genomic variation one usually find within a given bacterial species?

If I find the exact starting position (say 1152471) of the coding sequence of a given gene in the genome of a bacterium, is the genome of the bacterium in general stable enough so that I can expect to ...
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Full Sequence for Plasmid pMG101

I am trying to find the full plasmid sequence for pMG101. I have been looking through other papers that have sequenced this plasmid. The GenBank access numbers I got are the following: AY009372–...
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Quantifying the number of fragments from RAD library

I have a series of single-end reads from a RAD library of 48 uniquely tagged individuals in fastaq format. The data comes from a small MiSeq run. I want to know the number of unique fragments per ...
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Function and expression of pseudogenes

Can pseudogenes be transcribed into mRNA and translated into functional proteins, or should they be regarded as functionless mutated genes?
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106 views

How many dinosaur genes are in a chicken genome?

I read recently that we can "work back" to a dinosaur by selectively turning off certain genes in chickens, and we were able to create a chicken with a snout instead of a beak. How many dinosaur ...
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Is DNA sequencing coverage a function of sample purity?

How is coverage affected by the purity of a sample? And can coverage for a sample be affected by other things, like the library preparation or manner in which the sample was stored?
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24 views

Calling Alterations in Exome Data

What are the main technical differences between accurately calling somatic point mutations vs copy number variation (CNV) in exome data? Side note: would you need other -omic data to accurately infer ...
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20 views

Genomic distribution of tRNAs in eukaryotes

The title says it all. I'm doing a literature search trying to see what is widely known and/or well established. I've found a couple of mentions that tRNAs are dispersed throughout the entire nuclear ...
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41 views

Parameters of Variant calling analysis [closed]

What is the good or stringent parameter for variant calling. At present using the DP > 10 and Q > 30 for Variant calling. Is it ok.? Thanks
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How does one apply Bayesian inference to quantify a read the deeper you sequence?

For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule. What is the ...
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161 views

How is the size of a gene defined?

Is there an agreed definition as to how many nucleic acid bases constitute a gene? If not, why not? I'm not sure I understand how the exact sizes of genes are defined.
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Perplexing by the way of estimating the shared or different genes between humans and chimps

We share 98.5% genes with chimps (it means we have 98.5% same DNA sequeces ),so there is about one percent difference .It means we can approximately differ from them by one base pair every hundred ...
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What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?

This is a question which plagues many people and today I was wondering it myself while writing a grant. Indeed, I've seen many people use the terms interchangeably, but they are all very different ...
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What do recessive/dominant alleles actually mean in terms of modern genomics? [duplicate]

In Mendelian genetics, we discuss phenotypes, which are specified by the alternative versions of genes called alleles. In terms of peas, the phenotype "round pea" encoded by one allele of a gene is ...
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58 views

Current state of Gene Therapy [closed]

I am interested in learning about attempts to treat adult individuals suffering from a genetic disease in which the underlying changes in the DNA of the gene are understood. (i) Are there approaches ...
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What is gene density?

As per wikipedia definition, gene density is defined as: "In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in ...
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What is the best way to perform ultra-deep targeted sequencing of few samples?

I performed recent whole genome/exome sequencing in tumor samples and now I would like to take a few of these variants (say maximum 50 amplicons) to: 1) Validate them in the original samples 2) ...
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630 views

Are the number of base pairs in a given chromosome same between different individuals?

This is a basic question but I couldn't find an answer through a web search; hopefully this is the right place to ask. Is the number of base pairs in a particular chromosome the same in all ...
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47 views

Finding confidence level of miRNA disease associations

I'm an undergraduate computer engineering student, and I have a project about bioinformatics. In this manner, I need to find prediction( or association I'm not sure the correct terminology) confidence ...
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What further research can the result of gene variation detection be used for [closed]

We do a research on a particular cancer (for e.g. breast cancer). Now, we have a result for the gene variation detection (VCF file). What next steps do we need to do? We don't have a clear picture ...
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An elementary question for gene variation detection procedure in a paper

“Samples were divided into subtypes; each subtype was considered separately as a test set, using the remaining subtypes as the control. In our analysis, chromosome arms were subdivided into ...
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22 views

What the gene variation detection result can tell us about a cancer [duplicate]

We do a research on a particular cancer, now we have a result of the gene variation detection . What next steps do we need to do? we don't have a clear picture about this. Can you give us some ...
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38 views

How do biologists quantify “gene expression” in experiments?

I've read papers which contain statements such as "control of gene expression is critical in biological processes". How exactly does one quantify "gene expression"? Isn't gene expression an umbrella ...
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What physical traits are derived from the Neanderthal DNA in human DNA?

Some researches had found that Human DNA has a bit of Neanderthal DNA. So they suggested there would have been crossing between Homo sapiens and Neanderthals. Now the Neanderthal looked a bit ...
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47 views

How exactly are gaps defined in genomics?

My understanding is that when sequencing a genome, "gaps" refer to fragments which were not sequencing in the sequencer. Is this correctly? What are there other meanings to the term "gap"?
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How do high-throughput/NGS sequencers calculate quality scores?

I am confused as to how quality scores are actually calculated by DNA sequencers like Illumina. For each base call, some quality predictor value is computed, based on various properties of the ...
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Can both the overlapping genes (in opposite strands) produce proteins?

I have recognized that both the forward and reverse transcripts from a genomic location code for protein products. Both do occur/express in the tissue of interest. In order to eliminate by chance ...
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Which is the proportion of metagenomics reads that cannot be mapped in any genome?

I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable? I found a figure for viromics, which seems ...
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297 views

What is the relative power of GWAS studies in different species?

I would like to know of any publication studying the relative power of GWAS studies in different species. For example, I've seen reports that say genotyping and GWAS in dog breeds is much more ...
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Fold enrichment of chip-seq peaks in a broadpeak file [closed]

I have a broadpeak file that I downloaded from ENCODE. How can i compute the fold enrichment of the peaks in this file_format?
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Are there any major noticeable limitations to genome sequence compression methods that use reference templates?

Recently, I have been researching about big data analytics in biochemistry, and started wondering about how genome sequence compression could affect analysis. Of all the method listed on the ...
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138 views

Definition of Phenotype

I'm not a biologist but, I'm trying to enter molecular biology from a perspective. I have noticed that concept of genotype is quite well defined while ...
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Why did high A+T content create problems for the Plasmodium falciparum genome project?

The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
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Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
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RAD sequencing: choosing the appropriate enzyme?

I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
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Microbiome Data

How is it possible to access microbiome data like that found here? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the Human Biome Project. Thanks for any ...
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In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?

I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis. I also understand cloning can be a ...
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Where can I find DNA Sequence data for colon cancer

I am a computer scientist studying pattern recognition, and I am hoping to do some supervised learning on colon cancer. Unfortunately, I'm having a heck of a time finding DNA data in the following ...
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How does one find the corresponding SNPs in the pair of chromonosmes in a FASTA file?

You might say I'm an amateur bioinformatician, or trying to become one. I have a BAM file, from which I have succeeded, using UGENE , in extracting consensus data in FASTA format. I now see a single ...
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Good model for comparative genomics in relation to temperature adaptation

Can anyone suggest any highly related bacterial or parasitic species which live at very distinct temperatures, which might be a good model for comparison of genomes in regard to temperature adaptation....
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Inheritance of Huntington's disease

People with Huntington's disease have HTT genes with more than 37 copies of CAG repeat. The risk of extra copies being generated is higher during sperm formation than during ovum formation. Why is it ...
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A trivial question on the meaning of “relatives” in an article on horizontal gene transfer

Am I right in suggesting that by close relatives the author meant closely related species, or did he have individual organisms in mind? DETECTION OF HORIZONTAL GENE TRANSFER There are ...
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Comparative cost of RNA-seq vs sequencing full length cDNAs

I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data (...
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Genome Sequencing [closed]

Is Genome sequencing used to determine the relationship between two species that are believed to have a common line of descent? How accurate is this method if so? Are there more accurate methods ...
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Walkthrough Analyzing/Processing Genotyping Data for Association Studies

I need help outlining the data analysis process of analyzing genotyping data you get back from a Next Generation Sequencing experiment. Here are the steps I currently believe you go through, but I ...
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Walkthrough Illumina Genotyping

I would love help outlining a basic walkthrough of the wet-lab techniques for processing blood samples from patients, all the way to loading a BeadChip, to the part just before Next Generation ...
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What is meant by “the degree to which a gene is expressed” in an individual?

Here is an excerpt from a text that I was reading, Here is an example of microarray data. The idea is to take a group of different individuals and for each of them, you measure how much they ...
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30 views

How can a sequence be downloaded from UCSC genome browser

If I have genome coordinates is there a simple way to download the entire intervening sequence from the UCSC genome browser? I found some fancy way of using ftp but I can't figure it out.
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how to find full mitochondrial genome of plants in GenBank?

I am searching for full mitochondrial genome of a species of Malvaceae family. To be more specific, I need the genus Corchorus. ...