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

learn more… | top users | synonyms

5
votes
1answer
75 views

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 ...
3
votes
0answers
30 views

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 ...
2
votes
1answer
43 views

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 ...
0
votes
1answer
85 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 ...
2
votes
1answer
37 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 ...
3
votes
2answers
83 views

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 ...
2
votes
2answers
84 views

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 ...
1
vote
1answer
63 views

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 ...
2
votes
2answers
43 views

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 ...
1
vote
1answer
13 views

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 ...
5
votes
1answer
293 views

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 ...
0
votes
1answer
28 views

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 ...
6
votes
0answers
132 views

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 ...
0
votes
1answer
36 views

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 ...
0
votes
0answers
24 views

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 ...
1
vote
0answers
28 views

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 ...
3
votes
1answer
42 views

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 ...
0
votes
2answers
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.
0
votes
2answers
25 views

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. ...
3
votes
2answers
95 views

Do transposons usually jump from one chromosome to another?

If it is usual occurrence, does it mean that my one gene can change its location from one chromosome to another?
2
votes
1answer
144 views

What is pQTL and why do we need eQTL?

eQTLs are genomic loci that contribute to variation in expression levels of mRNAs (wikipedia). There is data out there that shows that ~60% of the time, the amount of mRNA in a cell is directly ...
2
votes
2answers
59 views

Database of medically validated SNPs

I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of ...
8
votes
3answers
463 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 ...
1
vote
1answer
14 views

Are Protocadherin Gamma Cluster transcripts considered separate genes?

The PDCH@ cluster of genes share exons and are therefore isoforms of each other. However, they are considered separate genes, by both HUGO and Ensembl. A "gene" is defined as "a locus of ...
2
votes
1answer
63 views

Are dogs affected by dwarfism?

My husband and I noticed a dog today that looked like a smaller version of a purebred Border Collie, although it didn't appear to be a puppy. It made us wonder if other animal species experience ...
1
vote
1answer
201 views

IC50 calculation [closed]

I am a computer science student and I'm in an internship at a genomics and biotechnologies research institute. My current task is to calculate the IC50 and the EC50 given a set of data as a table. ...
3
votes
1answer
109 views

Sex biased gene expression in the X chromosome

It has been shown that the X chromosome is frequently enriched for female biased genes, and has a deficit of male biased genes. For example in this paper, and this one. However, I'm struggling to ...
0
votes
2answers
574 views

What are the programming languages important to learn for a geneticist or bioinformatician? [closed]

I am interested in learning more about both genomics and bioinformatics, with emphasis on genomics. I was told after taking an introductory course of genomics that the programming language "R" and ...
1
vote
2answers
65 views

Punnet Square for Genotype Probabilities

I'm a computational physicist by trade, and today I was working with a student that is coding a simulation that requires the interactions of different genotypes to determine which phenotype will be ...
3
votes
1answer
695 views

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 ...
3
votes
1answer
88 views

What is the genomic position of HLA-B*1502 variation?

I've searched the position and SNP ID of HLA-B*1502 variation. However, I couldn't find that where this variant exactly located on genome or HLA-B gene.
6
votes
1answer
88 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 ...
0
votes
0answers
56 views

How do I select the sequence identity threshold in cd-hit to cluster proteins for core genome comparative analysis?

Can anyone suggest a method for selecting the sequence identity threshold for protein clustering in cd-hit? If I use too high of a threshold, then the number of protein clusters shared between three ...
3
votes
0answers
57 views

Degree of dosage compensation in Drosophila melanogaster

In this paper the authors state that the dosage compensation seen in Drosophila is approximately twofold, but they do not provide any source or numbers (as far as I can see) for this. What is the mean ...
0
votes
2answers
52 views

Mathematical modelling of omics data [closed]

I'm interested in modelling host-pathogen interactions using mathematics. I know there are good resources in Pubmed but seems I'm looking for a book or introductory reviews. My background in maths is ...
0
votes
0answers
14 views

What is the Magnitude of Nonspecific Oligo Binding at Low Temperatures

I am working on designing a protocol to capture genomic sequencing bound oligos (the part in question is identical to primer binding of genomic DNA during a PCR reaction). I'm wondering if anyone can ...
0
votes
1answer
108 views

(Genetics) Is a silencer the same as gene silencing (heterochromatin)?

Is silencer the same as gene silencing? I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a ...
0
votes
1answer
40 views

What does a read simulator do?

There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software
11
votes
2answers
435 views

Are there differences in DNA between humans of today and humans from 2000 years ago?

Are there any significant differences in our genome compared to the genes of our ancestors from 1000-2000 years ago? And if there are significant differences, do they result in significant ...
5
votes
2answers
44 views

Comparative Genomics

Are orthologs and paralogs examples of conserved genes? Orthologs are the genes or DNA that is present in 2 different species, having once been present in a common ancestor. It comes about by a ...
0
votes
0answers
21 views

Solid mouse (C57BL/6) WT primers

I am trying to get a good pair (or better yet, library of pairs) of primers that give me one band in WT mice (C57BL/6). Do you know where I could find such a thing? Alternatively, I thought of just ...
1
vote
0answers
51 views

Paired-end mapping exercise

Pair-end mapping (PEM) is a technique that allows to detect structural variants in DNA by obtaining paired-end reads and the comparison of their positions in a reference genome. Then among libraries ...
2
votes
1answer
43 views

Understanding conclusions that functional regions are under negative selection?

I am reading in notes for a comparative annotation lecture that : all DNA is subject to mutations most functional regions are under negative selection (ie., mutations are often deleterious) The ...
1
vote
0answers
56 views

“Gold standard” for CNV detection methods?

Is there a generally accepted "gold standard" for testing the performance of CNV detection methods? I'm interested both in learning about existing datasets that may serve as gold standards for CNV ...
1
vote
0answers
28 views

EMBOSS matcher and supermatcher - incongruent results?

I am trying to align a sequence to the mouse genome. I know a priori that part of my sequence should align to chromosome 9, but not all of it. I gathered that EMBOSS' ...
2
votes
0answers
16 views

Why there are two rounds of cytosine de-methylation in mammalian development?

I assume that the key biological meaning of cytosine de-methylation during germline development in germline progenitor cells is to reset imprinted genes and then set methylation pattern on these genes ...
1
vote
1answer
26 views

Could the proteome of E. coli be fluorescently labelled?

What proportion of the total number of proteins in E. coli could be fluorescently labelled for PALM/STORM imaging?
2
votes
1answer
103 views

Whole genome sequence analysis software

Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, ...
0
votes
1answer
58 views

Supercomputer and undergraduates [closed]

Is it common for an undergraduate to run their thesis (evolutionary genomics) in a supercomputer? In my country, few supercomputers exist, but I'm not sure how it is for bachelors in the US or Europe. ...
2
votes
0answers
30 views

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) ...