BOL: Related items

BIGRE Lab

Sun, 17 Nov 2013 10:35:49 -0600

The Laboratoire de Bioinformatique des Génomes et des Réseaux (Genome and Network Bioinformatics) is specialized in the conception, implementation, evaluation and application of bioinformatics approaches for the analysis of genome, transcriptome, proteome and metabolism.
Our main activities include

Analysis of regulatory sequences (RSAT project)
Classification and analysis of mobile genetic elements (ACLAME project).
Analysis of molecular interaction networks (NeAT project)
Inference of metabolic pathways from genomic and post-genomic data
(metabolic pathfinding, see also metabolic pathfinding in NeAT)
Critical assesment of protein interactions (CAPRI)

Lab Page http://www.bigre.ulb.ac.be/

Genome U-Plot: a whole genome visualization

Rahul Nayak — Fri, 13 Jul 2018 19:50:41 -0500

Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities.

https://github.com/gaitat/GenomeUPlot

Address of the bookmark: https://github.com/gaitat/GenomeUPlot

GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences

Jit — Fri, 28 Sep 2018 09:35:10 -0500

GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:

Step 1. Run mugsy to get multiple sequence alignment results.
Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permutations.
Step 4. Generate pairwise genome rearrangement scenarios and find repeats at the breakpoints of each rearrangement events.

https://github.com/DanwangJessica/GRSR

Address of the bookmark: https://github.com/DanwangJessica/GRSR

ncbi-datasets-cli -- Quickstart: command line tools !

Jit — Tue, 07 Dec 2021 02:51:26 -0600

Install and use the NCBI Datasets command line tools

The NCBI Datasets datasets command line tools are datasets and dataformat .

Use datasets to download biological sequence data across all domains of life from NCBI.

Use dataformat to convert metadata from JSON Lines format to other formats.

Conda download:

https://anaconda.org/conda-forge/ncbi-datasets-cli

Buld Download

https://www.ncbi.nlm.nih.gov/datasets/builder/?tax_id=29979

Address of the bookmark: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/

VCF Compare !

Rahul Nayak — Wed, 19 Jan 2022 10:30:14 -0600

compare two BWA mapping methods with the online hg18-mapped data

We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam>, aligned to the b36/hg18 reference genome)

Address of the bookmark: https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare

The 8000 years old Tibetian gene mutation !!!

Neel — Wed, 20 Aug 2014 21:57:44 -0500

A new study has provided insight into how gene mutation around 8,000 years ago helped Tibetans' to survive in the thin air on the Tibetan Plateau, where an average elevation is of 14,800 feet.

A study led by University of Utah scientists is the first to find a genetic cause for the adaptation, a single DNA base pair change that dates back 8,000 years and demonstrate how it contributes to the Tibetans' ability to live in low oxygen conditions.

About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88 percent of Tibetans have the genetic variation, and it was virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.

In those without the adaptation, low oxygen caused their blood to become thick with oxygen-carrying red blood cells, an attempt to feed starved tissues, which could cause long-term complications such as heart failure. The researchers found that the newly identified genetic variation protected Tibetans by decreasing the over-response to low oxygen.

Reference: http://www.nature.com/nature/journal/v512/n7513/abs/nature13408.html

Dynamic chromosome breakpoints !!!

Jitendra Narayan — Wed, 13 Aug 2014 18:38:10 -0500

Cell division involves the distribution of identical genetic material, DNA, to two daughters’ cells. During this process, duplicated deoxyribonucleic acid (DNA) goes through a condensation and decondensation process. This is followed by nuclear envelope dissolution, mitotic spindle assembly, migration of the sister chromatid pairs to the metaphase plate, division and segregation of identical sets of chromosomes into daughter nuclei and nuclear envelope reformation.

The vital metaphase stage of cell division, when the sister chromatids migrated to the centre and lined up in a row, and pulled apart using attached microtubules in such a way that half the DNA ends up in each daughter cell. However, before the mitotic spindle‐mediated movement gets start and pulled DNA apart, the chromosomes are free to undergo recombination which involves the exchange of genetic material either between multiple chromosomes or between different regions of the same chromosome.

During recombination, the precise breakage of each strand, exchange between the strands, and sealing of the resulting recombined molecules happens. The “chromosomal breakpoints” refers to these places where they break. Mostly, this process occurs with a high degree of accuracy at high frequency in both eukaryotic and prokaryotic cells. But occasionally this “break and sealing/ break and reattach” process goes wrong and the reattachment happens in the wrong place which usually create disaster (with few exceptions).These chromosome disaster or abnormalities involve the gain, loss or rearrangement of visible amounts of genetic material during cell division. These abnormalities are of two type, the first one is numerical abnormalities where severe disorders are caused by the loss or gain of whole chromosomes, which affect the copy number of hundreds or even thousands of genes. The second are structural abnormalities which can be unbalanced or balanced. The former are similar to numerical abnormalities in that genetic material is either gained or lost. The natural defects in chromosome segregation are linked to cancer and several genetic diseases (http://en.wikipedia.org/wiki/List_of_genetic_disorders). Therefore, the enzymes involved in regulating cell division are still the attractive drug targets for many diseases.

Apart from certain chromosome abnormalities, these “crossing over” of segments of maternal and paternal chromosomes to form hybrid chromosomes have some evolutionary importance and considered as a driver of genetic variation. Moreover, the chromosome breakage in evolution is considered to be non-random in nature(http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020014). In addition the study of breakpoint regions and non-breakpoint (stable) regions of chromosomes indicates both the regions evolved in distinctly different ways ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/). These breakage may lead to genetic diseases or participate to chromosomal rearranmgnets and contributed in development of new species.

I will try to explain the genome hotspots/Evolutionary Breakpoint Regions(EBRs)/fragile regions/weak fragments/ in my next blog.

Software for recombination detection:

RAT http://cbr.jic.ac.uk/dicks/software/RAT/

Breakpointer https://github.com/ruping/Breakpointer

DRP http://web.cbio.uct.ac.za/~darren/rdp.html

RB-finder http://www.ncbi.nlm.nih.gov/pubmed/18707535

LDhat2.0 http://ldhat.sourceforge.net/LDhat2.0/instructions.shtml

Reference:

http://www.nature.com/scitable/topicpage/genetic-recombination-514#

Image: Wikipedia , sciencelearn.org.nz

Recommended Articles:

http://www.friendshipcircle.org/blog/2012/05/22/13-chromosomal-disorders-youve-never-heard-of/

http://web.udl.es/usuaris/e4650869/docencia/segoncicle/genclin98/recursos_classe_%28pdf%29/revisionsPDF/chromosyndromes.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775595/table/T2/

http://learn.genetics.utah.edu/content/disorders/chromosomal/

http://www.ncert.nic.in/html/learning_basket/biology/cc&cd.pdf

Nieduszynski Group

Fri, 26 Sep 2014 19:35:06 -0500

Complete, accurate replication of the genome is essential for life. All chromosomes in eukaryotic cells must be duplicated and then segregated to daughter cells to ensure genetic integrity and produce the large number of cells that make up a multicellular organism. We are using genetic, genomic and computational methods to understand how chromosome replication is regulated to ensure genome stability. By focusing on the basic biology that underpins cell growth and division we aim to provide new insights that may help our understanding of diseases such as cancer and congenital disorders.

More http://www.nieduszynski.org/index.php
http://www.path.ox.ac.uk/research/cell-biology-and-pathology/conrad-nieduszynski-group

A 3D Map of the Human Genome

Fri, 12 Dec 2014 22:27:55 -0600

Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell.

Sequencing By Xpansion

Jitendra Narayan — Wed, 17 Jun 2015 20:58:11 -0500

Sequencing By Xpansion (SBX) is a DNA sequencing method that uses a simple biochemical reaction to encode the sequence of a DNA molecule into a highly measurable surrogate called an Xpandomer. This single molecule approach produces enough Xpandomer in a single drop reaction to sequence an entire human genome 1000X over. To achieve this, an Xpandomer replaces each DNA sequence with a sequence of large, high signal reporter molecules using the SBX molecular expansion technology. The DNA sequence is then read out as the Xpandomer reporters pass sequentially through a nanopore detector. SBX is a molecular engineering platform that benefits from core design principles that separate the multiple molecular functions. This systems approach enables efficient development and incorporation of improvements to SBX and is key to reconfiguring and optimizing Xpandomer measurement for different detection platforms.

http://www.stratosgenomics.com/stratos-genomics-technology