BOL: Related items

Molecular Genetics Lecture

Rahul Agarwal — Fri, 27 Sep 2013 04:24:45 -0500

"Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories."

"Robert Sapolsky is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia

Address of the bookmark: http://www.youtube.com/watch?v=_dRXA1_e30o

Edit DNA !!!

Jit — Wed, 05 Mar 2014 02:27:54 -0600

A genome-engineering tool known as Crispr may allow scientists to alter the DNA of humans, animals and plants, a research breakthrough that promises to make a significant impact on science and fighting diseases, according to a March 3 story in the New York Times. Scientists hope Crispr might also be used for genomic surgery, as it were, to correct errant genes that cause disease.

A rescently publication paper ( http://jb.asm.org/content/169/12/5429.long )shows significance of an unusual repeated DNA sequences next to a gene in a common bacterium, and their scientific significance. The sequences, it turns out, are part of a sophisticated immune system that bacteria use to fight viruses. And that system, whose very existence was unknown until about seven years ago, may provide scientists with unprecedented power to rewrite the code of life. This means a genome can be edited, much as a writer might change words or fix spelling errors. It allows “customizing the genome of any cell or any species at will,”.

Reference:

http://www.prweb.com/releases/2014/03/prweb11636031.htm

http://www.nytimes.com/2014/03/04/health/a-powerful-new-way-to-edit-dna.html?hpw&rref=health

http://jb.asm.org/content/169/12/5429.long

Scripted DNA !!!

Jit — Mon, 17 Aug 2015 17:44:04 -0500

As per bioinformatician DNA is partially scripted ;) You dont believe in it. Please have a look at image carefully:)

DNA testing companies around the globe !

Jit — Thu, 13 Jul 2017 04:44:03 -0500

It was realized in the 1940s that DNA molecules are passed down through the generations of a family. In 1953 Watson and Crick elucidated the chemical structure of this molecule as a twisted ladder (a ‘helix’) made of two strands. DNA occurs in all the cells of our body, it is our blueprint! The strands of DNA contain information in the form of a code, which in turn determines our individual traits and characteristics. This code, the genetic code, is the order of four types of DNA building block. When the two strands of DNA separate, each building block (‘base’) accurately templates a corresponding base on the newly made strand of DNA so that information is not lost but is instead duplicated and preserved.

Testing for similarities between DNA (deoxyribonucleic acid) samples from two people allows family relationships to be established – or disproved – to an extraordinarily high degree of certainty. A common use for a DNA test is to establish if a man is the biological father of a child; this is known as a paternity test. However, there are other uses for the science of DNA testing (also called genotyping), these include forensic analysis of human DNA samples, and tracking relationships amongst domesticated animals.

The order in which the bases occur in DNA is referred to as the DNA sequence. Each person is unique and just as people differ in their fingerprints, they also have a unique and slightly different DNA sequence. Half of a person’s DNA is received from their mother, and half is received from the father. However, while fingerprints have no value for establishing family relationships, the minor variations in DNA sequence are extraordinarily useful for this purpose. All cells of our body contain DNA, skin cells from the lining of the cheek provide a simple and convenient source of material.

DNA is purified from these cells and the minor variations are read out as a type of bar-code by a machine. When the net DNA ‘barcodes’ from family members are lined up next to each other it becomes clear when a child is related to biological parents because half the stripes in the bar-code like signature will line up with those of the mother, and half will line up with those of the father. On the other hand, in the absence of a biological relationship, the DNA signatures from a child and from a potential parent are not found to have 50% in common. It may be appreciated that DNA testing is the most convenient and scientifically accurate method of determining relationships between people.

Following are the list of companies who qssist in DNA testing:

DNA testing companies

23andMe (admixture, adoption, deep ancestry, genealogy) (health and trait reports also available in some countries)
24 genetics (admixture, exome sequencing, health, paternity, pharmacogenetics, whole genome sequencing) A company catering for the Spanish market
African Ancestry (deep ancestry)
AfricanDNA (FTDNA affiliate) (admixture, deep ancestry, genealogy)
AncestrybyDNA (admixture, deep ancestry)
AncestryDNA, a subsidiary of Ancestry.com (admixture, adoption, genealogy)
Atlas Biomed (deep ancestry, diet, health and traits, sport) A test catering for the Russian market
BritainsDNA (formerly Ethnoancestry) (admixture, deep ancestry)
Centrillion Biosciences (aka TribeCode) (admixture, deep ancestry)
CymruDNAWales - see BritainsDNA
Dante Labs (exome sequencing, health, whole genome sequencing) A test aimed at the European market
DNA Ancestry and Family Origin (FTDNA affiliate in the Middle East) (admixture, adoption, deep ancestry, full mtDNA sequencing, genealogy)
DNA Consultants (admixture, deep ancestry)
DNA Tribes (admixture)
DNA Worldwide (formerly a FTDNA partner. See also Living DNA)
Ethnoancestry - see BritainsDNA
Family Tree DNA (admixture, adoption, deep ancestry, full mtDNA sequencing, genealogy, Y chromosome sequencing)
Full Genomes Corporation (whole genome sequencing, Y-chromosome sequencing)
Gene by Gene - the parent company of Family Tree DNA which now incorporates the companies previously known as DNA Traits, DNA DTC and DNA Findings (research, health, exome sequencing, whole genome sequencing)
Genebase (deep ancestry, genealogy)
GenoTek (admixture, genealogy, diet and fitness, family planning, health, talents and sports) A company catering for the Russian market
Genographic Project (admixture, deep ancestry)
Genos Research Inc (DTC whole exome sequencing; consumer focused healthcare big data spin out from Complete Genomics; Note: no genetic genealogy focus or tools)
Guardiome (admixture, whole genome sequencing and interpretation)
Helix (exome sequencing) US supplier of the Genographic Project Geno 2.0 Next Generation test
iGENEA (FTDNA affiliate) (admixture, deep ancestry, genealogy)
IrelandsDNA - See BritainsDNA (formerly Ethnoancestry)
MyDNA Global - a new name for BritainsDNA
Living DNA (admixture, deep ancestry) See also DNA Worldwide
MyHeritage DNA (admixture, genealogy)
Oxford Ancestors (deep ancestry)
Roots for Real (admixture, deep ancestry)
ScotlandsDNA - (formerly Ethnoancestry) (admixture, deep ancestry)
Sorenson Genomics (laboratory services)
Sure Genomics (whole genome sequencing and interpretation)
TribeCode See Centrillion Biosciences
Veritas Genetics (whole genome sequencing and interpretation)
Xcode (Diet and Fitness, Precision medicine, Genotyping, Sequencing, Interpretation)
YorkshiresDNA - See BritainsDNA (formerly Ethnoancestry)
WeGene (admixture, deep ancestry, health, sports, traits) A test tailored for the East Asian market
YSEQ (custom Y-SNPs, Y-STRs, SNP panels, whole genome sequencing)

Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Jit — Tue, 26 Dec 2017 22:23:39 -0600

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

Address of the bookmark: https://ncbi.github.io/magicblast/

ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

Seema Singh — Mon, 30 Apr 2018 04:38:40 -0500

ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

The El-Sherif Group, Chair of Developmental Biology, Department of Biology - PhD Position

Sun, 19 Jan 2020 10:06:37 -0600

El-Sherif lab studies how genes are regulated to mediate patterning in Development. We use live and super-resolution imaging in addition to computational modeling to understand transcription dynamics at the single-cell level in three model systems: the fruit fly Drosophila melanogaster, the beetle Tribolium castaneum, and embryonic bodies derived from embryonic mouse stem cells.

In this project, you will use single-molecule techniques to label mRNA and DNA in (live and fixed) Drosophila embryos and fixed embryonic bodies. You will also use super-resolution microscopy to visualize protein condensates. Co-localization dynamics reflecting DNA-protein bindings and DNA looping events will be detected, analyzed, and used to test computational models of gene transcription.

Qualification:
MSc degree (or equivalent) in Biology, Biophysics, or Bioengineering

Experience in one or more of these areas: (1) molecular cloning, (2) imaging, (3) image analysis (using Matlab/Python/Java), (4) microfluidics, and (5) computational modeling.

How to Apply?
Send (1) your CV, (2) summary of research experience, and (3) email addresses of at least 2 references to ezzat.el-sherif@fau.de. Title your email ‘Transcription PhD Position’.

salary Grade.: E13
Total Time: 3 Jahre
Start: 01.01.2020.
End: 31.3.2020.

Address:
Dr. El-Sherif, Ezzat
Department Biologie
Professur für Zoologie (Entwicklungsbiologie) (Prof. Dr. Klingler)
Telefon 09131/85-28068, Fax 09131/85-28040, E-Mail: ezzat.el-sherif@fau.de

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures

Poonam Mahapatra — Thu, 04 Jun 2020 23:19:07 -0500

The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users are required to provide the three-dimensional (3D) structures of the two molecules to be docked.

Address of the bookmark: http://huanglab.phys.hust.edu.cn/hnadock/

ExRec: Exclusion of Recombined DNA

LEGE — Wed, 27 Mar 2024 20:48:26 -0500

ExRec (Exclusion of Recombined DNA) is a Python pipeline that implements the four-gamete test to filter out recombined DNA sites from up to thousands of DNA sequence loci. The pipeline consists of five standalone applications: the first two convert folders of NEXUS or PHYLIP files into the standard input file for the main program that conducts the four-gamete filtering procedures. The pipeline outputs recombination-filtered data in concatenated NEXUS and PHYLIP formats and a tab-delimited table containing descriptive statistics for all loci and the results. This software also allows the user to output the longest non-recombined sequence blocks from loci (current best practice) or randomly select non-recombined blocks from loci (a newer approach). Two other applications in the package convert the recombination-filtered data into single-locus NEXUS or PHYLIP files. The ExRec package can thus facilitate species delimitation, species tree, and historical demography studies by providing loci that better meet the no-recombination assumption in coalescent-based analyses.

Link to the article: https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad174/7455250?searchresult=1

Link to the software:
https://github.com/Sammccarthypotter/ExRec

Address of the bookmark: https://github.com/Sammccarthypotter/ExRec

UniqueKmer: Generate unique KMERs for every contig in a FASTA file

Abhi — Fri, 17 Dec 2021 00:08:15 -0600

Generate unique k-mers for every contig in a FASTA file.

Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands).

This tool accepts the input of a FASTA file consisting of many contigs, and extract unique k-mers for each contig.

The output unique k-mer file and Genome file can be used for fastv: https://github.com/OpenGene/fastv, which is an ultra-fast tool to identify and visualize microbial sequences from sequencing data.

https://github.com/OpenGene/UniqueKMER

Address of the bookmark: https://github.com/OpenGene/UniqueKMER