BOL: Related items

Flu Attack! How A Virus Invades Your Body

Thu, 22 Aug 2013 08:09:51 -0500

When you get the flu, viruses turn your cells into tiny factories that help spread the disease. In this animation, NPR's Robert Krulwich and medical animator David Bolinsky explain how a flu virus can trick a single cell into making a million more viruses. See and hear the rest of the story on NPR.org: http://www.npr.org/templates/story/story.php?storyId=114075029 Credit: Robert Krulwich, David Bolinsky, Jason Orfanon

NCBI to assist in Virus Hunting Data Science Hackathon

BioStar — Thu, 15 Nov 2018 12:55:01 -0600

NCBI Hackathon are pleased to announce the second installment of the SoCal Bioinformatics Hackathon. From January 9-11, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University!

NCBI Hackathon specifically looking for folks who have experience in computational virus hunting or adjacent fields to identify known, taxonomically-definable and novel viruses from a few hundred thousand metagenomic datasets that we’ll put on cloud infrastructure. This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. If this describes you, please apply! The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).

https://ncbiinsights.ncbi.nlm.nih.gov/2018/11/09/ncbi-sdsu-virus-hunting-data-science-hackathon-january-2019/

MPXV Bookmarks

BioStar — Mon, 19 Dec 2022 01:58:20 -0600

MPVX infection across the globe

https://www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.html

Address of the bookmark: https://www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.html

Influenza animation - flu virus mechanism

Thu, 17 Oct 2013 19:43:13 -0500

Animation of the mechanism of an influenza virus and how Crucell's antibodies target the HA1 proteins on the virus and prevent further spread of influenza. Client: Crucell Direction, Design & Animation: Daniel Lim, 2Preform Music & Sound Design: Javier Barrero, Logical Disorder Production Company: David Hager, All Terrain Media

fastv - detect virus

Jit — Sat, 11 Dec 2021 08:04:10 -0600

fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect viral infectious diseases, like COVID-19. This tool supports both short reads (Illumina, BGI, etc.) and long reads (ONT, PacBio, etc.)

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

WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.

Neel — Thu, 23 Sep 2021 14:31:06 -0500

Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community metagenomes remains an open problem. To address this, we developed WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.

Address of the bookmark: http://huttenhower.sph.harvard.edu/waafle

Snakemake—a scalable bioinformatics workflow engine

Jit — Sun, 02 Sep 2018 16:32:42 -0500

Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.

Address of the bookmark: https://bioconda.github.io/recipes/snakemake/README.html

Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes

LEGE — Wed, 21 Feb 2024 06:13:08 -0600

Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. Our goal was to make it straightforward to work from a combination of input sources including annotated contigs in Genbank format and FASTA files containing CDSs. It uses several state of the art inference methods for orthology inference, either based on HMM profiles or de novo inference of orthogroups. Through the use of OrthoSNAP, many additional ortholog alignments can be generated from multi-copy gene families. For phylogenetic inference, users can choose a supermatrix approach and/or gene tree inference followed by supertree reconstruction. Users can specify a range of alignment filtering settings to retain high-quality alignments for phylogenetic inference. The workflow produces a detailed report that, in addition to the phylogenetic results, includes a range of diagnostics to verify the quality of the results.

Address of the bookmark: https://github.com/rbturnbull/orthoflow

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

Opera: An optimal genome scaffolding program

Jit — Mon, 27 Nov 2017 10:18:20 -0600

Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes.

Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y.

Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

Address of the bookmark: https://sourceforge.net/projects/operasf/