<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38053?offset=420 https://bioinformaticsonline.com/bookmarks/view/44483/baclife-an-automated-genome-mining-tool-for-identification-of-lifestyle-associated-genes Fri, 15 Mar 2024 04:59:14 -0500 https://bioinformaticsonline.com/bookmarks/view/44483/baclife-an-automated-genome-mining-tool-for-identification-of-lifestyle-associated-genes <![CDATA[bacLIFE: an automated genome mining tool for identification of lifestyle associated genes]]> bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gene clusters associated with each lifestyle detected. This whole process is divided into different modules:

  • Clustering module Predicts, clusters and annotates the genes of every input genome
  • Lifestyle prediction Employs a machine learning model to forecast bacterial lifestyle or other specified metadata
  • Analitical module (Shiny app) Results from the previous modules are embedded in a user-friendly interface for comprehensive and interactive comparative genomics.

You can find the complete wiki here [https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki]

Address of the bookmark: https://github.com/Carrion-lab/bacLIFE

]]> BioStar https://bioinformaticsonline.com/blog/view/45278/the-day-we-began-reading-the-dna-of-the-world Sat, 05 Sep 2026 01:43:21 -0500 https://bioinformaticsonline.com/blog/view/45278/the-day-we-began-reading-the-dna-of-the-world <![CDATA[The Day We Began Reading the DNA of the World]]> Picture waking up and knowing that in one lab, a scientist is reading the DNA of a whale. In another, a team is sequencing a rare plant. Meanwhile, researchers in India are decoding the genomes of different human populations.
 
Many organisms. Many countries. All share one remarkable goal: to understand the genetic story of life.
DNA is nature's instruction manual, written with just four letters: A, T, C, and G. For years, scientists could only read small sections of this huge book. Now, new sequencing technology lets us read entire genomes like never before.
 
One of the most ambitious projects is the Earth BioGenome Project (EBP). Its goal is to create reference genomes for about 1.5 million known eukaryotic species. This project links genome research across continents, species, and scientific fields.
 
But this story goes beyond just animals and plants.
 
A New Chapter in Human Genomics
 
Large human genome projects are changing how we understand our own genetic diversity.
India's GenomeIndia project has sequenced thousands of people from different populations. This work is uncovering genetic variation that global databases have often missed.
 
Similar population-scale effSimilar large-scale projects are happening worldwide. The All of Us Research Program in the United States, Europe's 1+ Million Genomes initiative, South Korea's national genomic data program, and projects in Saudi Arabia, Australia, and Singapore are all building huge genomic resources.collect DNA.
 
The real goal is to link genomes with health, disease, and other biological information. This creates a base for more accurate research and, in time, more personalized medicine.
 
A Race Against Time
 
There is also an important twist.
 
We are sequencing Earth's biodiversity even as many species face growing environmental threats.
A genome alone cannot save a species, but it does keep important information about its biology, evolution, and genetic diversity. This knowledge helps scientists understand risks, guide conservation, and find traits that could help agriculture or medicine.
 
Projects like the Darwin Tree of Life, which studies species in Britain and Ireland, and the African BioGenome Project, which is growing genomics work across Africa, are key parts of this worldwide effort.
 
Projects to Watch
  1. Earth BioGenome Project (EBP) - A global effort to sequence and annotate roughly 1.5 million known eukaryotic species and create a comprehensive reference library of Earth's biodiversity.
  2. Vertebrate Genomes Project (VGP) - Focuses on producing high-quality reference genomes for vertebrate species, providing a major foundation for the wider Tree of Life.
  3. Darwin Tree of Life - A UK and Ireland initiative aiming to sequence approximately 70,000 species, creating a detailed genomic map of regional biodiversity.
  4. African BioGenome Project (AfricaBP) - A pan-African initiative focused on sequencing Africa's biodiversity while strengthening genomics and bioinformatics capacity across the continent.
  5. European Reference Genome Atlas (ERGA) - A European effort to generate high-quality reference genomes for Europe's biodiversity and connect national sequencing efforts.
  6. Canada BioGenome Project - Building reference genomes for Canadian biodiversity, supporting conservation, research and the study of ecosystems.
  7. California Conservation Genomics Project - Uses genomics to understand and protect California's biodiversity and help inform conservation decisions.
  8. Bat1K - An ambitious global effort to sequence the genomes of all known bat species, helping scientists study their evolution, longevity, immunity and unique biology.
  9. Bird 10,000 (B10K) - A global project aiming to create genome resources covering the world's bird diversity and reconstruct avian evolutionary history.
  10. Global Invertebrate Genomics Alliance (GIGA) - Builds genomic resources for the enormous and genetically diverse world of invertebrates.
  11. GenomeIndia - India's national human-genome initiative, designed to capture the country's extraordinary population diversity and create a reference resource for Indian genomics.
  12. All of Us Research Program - A US national research program combining genomic information with health and lifestyle data at population scale.
  13. 1+ Million Genomes / Genome of Europe - A European effort to enable secure, cross-border use of genomic and health data and develop genome-scale resources involving more than one million people.
  14. Korea National Integrated Bio Big Data Project - South Korea's large-scale national effort combining genomic and health information from a very large population cohort.
  15. Saudi Genome Program - A national genomics initiative focused on genetic diseases, population genomics and precision medicine in Saudi Arabia.
  16. Australian Genomics / Genomics Health Futures Mission - Australia's growing investment in genomic medicine, rare disease research and population-scale health genomics.
The Library of Life
 
The fuThe future of genomics is not just about sequencing one genome at a time. Now, it is about creating a worldwide network of genomes—human and non-human, individual and species—linked by powerful databases and advanced computational tools.ine a library without shelves.
 
In this library, the books are genomes. The pages are made of DNA. Scientists and machines are the readers. And this library is still being written. Each genome sequenced today adds a new page to the story of life and helps us better understand our place in it.
]]> Jitendra Narayan https://bioinformaticsonline.com/opportunity/view/4004/33rd-annual-convention-of-indian-association-for-cancer-research-from-13th-to-15th-february-2014 Tue, 27 Aug 2013 10:37:08 -0500 <![CDATA[33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014]]> RGCB is organizing the 33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014 with the theme "Discovery, Innovation and Translation in Cancer Research"

Kindly log on to conference website http://rgcb.res.in/IACR2014 for further details and timely updates and registration. We shall truly appreciate if the same be circulated among your friends, scholars and students encouraging them to participate in the meet.

http://210.212.237.38/iacrconference/

]]> https://bioinformaticsonline.com/videolist/watch/3917/the-story-of-you-encode-and-the-human-genome Sat, 24 Aug 2013 18:49:03 -0500 https://bioinformaticsonline.com/videolist/watch/3917/the-story-of-you-encode-and-the-human-genome <![CDATA[The Story of You: ENCODE and the human genome]]>

Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE

]]> https://bioinformaticsonline.com/videolist/watch/4960/genome-epigenome-new-understanding-of-the-pathogens-in-your-food Fri, 27 Sep 2013 11:30:45 -0500 https://bioinformaticsonline.com/videolist/watch/4960/genome-epigenome-new-understanding-of-the-pathogens-in-your-food <![CDATA[Genome + Epigenome = New Understanding of the Pathogens in Your Food]]> UC Davis's Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close genomes and analyze methylation; Weimer reports that his team has already discovered new epigenetic modifications in Salmonella and Listeria with the technology. www.pacb.com/microbe]]> https://bioinformaticsonline.com/file/view/8650/bioinformatician-duties-and-jobs Wed, 05 Mar 2014 14:32:26 -0600 https://bioinformaticsonline.com/file/view/8650/bioinformatician-duties-and-jobs <![CDATA[Bioinformatician duties and jobs !!!]]> Needle in a haystack ... ohh yes this is what bioinformatician do. We handle and analyse, Terabytes and Petabytes of genomic data on daily basis.

]]> Jitendra Narayan https://bioinformaticsonline.com/videolist/watch/11249/how-to-sequence-the-human-genome-mark-j-kiel Fri, 30 May 2014 13:24:11 -0500 https://bioinformaticsonline.com/videolist/watch/11249/how-to-sequence-the-human-genome-mark-j-kiel <![CDATA[How to sequence the human genome - Mark J. Kiel]]> View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.]]> https://bioinformaticsonline.com/blog/view/14011/dynamic-chromosome-breakpoints Wed, 13 Aug 2014 18:38:10 -0500 https://bioinformaticsonline.com/blog/view/14011/dynamic-chromosome-breakpoints <![CDATA[Dynamic chromosome breakpoints !!!]]> 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.

image

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.

 

 

image

 

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

]]> Jitendra Narayan https://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome Fri, 12 Dec 2014 22:27:55 -0600 https://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome <![CDATA[A 3D Map of the Human Genome]]> 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.]]> https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics Thu, 18 Dec 2014 11:05:42 -0600 https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics <![CDATA[Google Genomics]]>

  • Explore genetic variation interactively. Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.

  • Process big genomic data easily. Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.

  • Use Google's infrastructure and big data expertise. Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.

  • Support emerging global standards. Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

    • Address of the bookmark: https://cloud.google.com/genomics/

    ]]>     Tenzin Paul