BOL: Related items

ForBio and UiB course: Introduction to phylogenetic methods

Rahul Nayak — Mon, 16 Dec 2019 09:39:12 -0600

The is an introductory course that is aimed at students who will need to preform phylogenetic analyses in their work, but who have little or no experience with phylogenetic analyses. The ForBio component of the course is focused on the practical aspects of phylogenetic analyses and students that have not attended the theoretical part of the course are expected to have read the relevant literature. The course will cover all basic aspects of phylogenetic analyses with emphasis on use of DNA data. Students will learn how to prepare their data, explore its properties and how to analyze it using distance, parsimony, likelihood and Bayesian methods. In the last two days students will also get an introduction to molecular dating with focus on the use of BEAST and to comparative methods used to study the evolution of discrete and continuous traits.

https://www.forbio.uio.no/events/courses/2020/Bergen_Phylogenetics_2020.html

ForBio travel grants
We have changed our travel grants rules. ForBio offers both incoming and outgoing travel grants to fund collaborations between ForBio members based in Norway and taxonomic experts up to NOK 14,000. Grants are given for taxonomic training with relevance to the main research project of the applicant, and aim to allow the student to do taxonomic research with specific experts, work with particular collections, or learn new preparation techniques directly from experts. Participation in external courses, conferences, fieldwork or other kinds of activities which are not classified as expert-in-training visits are no longer eligible for support. There are two application deadlines: March 1st 2020.

Swabs to Genomes: A Comprehensive Workflow

Rahul Nayak — Sun, 10 Aug 2014 03:01:21 -0500

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

Address of the bookmark: https://peerj.com/preprints/453.pdf

CLAW: Chloroplast Long-read Assembly Workflow

LEGE — Wed, 21 Feb 2024 12:37:46 -0600

CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read libraries (e.g., an Oxford Nanopore Technologies MinION read library derived from photosynthetic tissue), for assembly with Flye and/or Unicycler. CLAW was designed with the novice bioinformatician in mind - it is easy to install and easy to use, requiring only minimal user input.

Address of the bookmark: https://github.com/aaronphillips7493/CLAW

VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening

BioStar — Sat, 13 Jun 2020 13:03:09 -0500

related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (such as SLURM).

Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks:

They use the same core technology regarding the workflow management and parallelization, and they can be used individually or in concert with each other. Additional versions are expected to arrive in the future.

https://github.com/VirtualFlow

https://www.nature.com/articles/s41586-020-2117-z?

Address of the bookmark: https://virtual-flow.org/

ENCODE3: A collection of research articles and related content describing the Encyclopedia of DNA Elements, its datasets and tools.

Shruti Paniwala — Sat, 08 Aug 2020 08:25:21 -0500

How cells, tissues and organisms interpret the information encoded in the genome has vital implications for our understanding of development, health and disease. Launched in 2003, the ENCyclopedia Of DNA Elements (ENCODE) project has the aim of mapping the functional elements in the human genome (later expanded to include model organisms).

During the first phase of ENCODE, published in 2007, microarray-based technologies were used to detect regions associated with transcription factors, certain histone modifications and open chromatin within a pre-specified 1% of the human genome.

ENCODE’s second phase saw a switch to sequencing-based technologies, the addition of new assay types and the analysis of functional elements genome-wide, described in a collection of research articles in 2012.

The Encyclopedia paper of ENCODE 3, published in Nature, gives an overview of the various assays that were performed in human and mouse cell lines and tissues and describes a Registry of human and mouse candidate cis-regulatory elements (cCREs).

More at https://www.nature.com/immersive/d42859-020-00027-2/index.html

NCBI Datasets pages

BioStar — Wed, 12 Jul 2023 06:29:31 -0500

Update! Assembly and Genome record pages now redirect to new NCBI Datasets pages. NCBI Datasets is a new resource that makes it easier to find and download genome data. Learn more: https://ncbiinsights.ncbi.nlm.nih.gov/2023/07/11/ncbi-datasets-genome-assembly-pages/ #NCBICGR

Effective July 10, 2023, NCBI’s Assembly and Genome record pages now redirect to new NCBI Datasets pages. As previously announced, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.  

The following pages have been updated:

The NCBI Assembly record pages now redirect to the new NCBI Datasets Genome record pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST. 
The NCBI Genome record pages now redirect to the NCBI Datasets Taxonomy record pages that provide a taxonomy-focused portal to genes, genomes, and additional NCBI resources.

During this transition, you will have the option to return to the legacy Genome and Assembly record pages. We will remove the legacy pages in early 2024. 

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Abhimanyu Singh — Fri, 02 Nov 2018 08:16:27 -0500

Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life.

Address of the bookmark: http://ancestralgenomes.org/

ClueGO: a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes

BioStar — Thu, 13 Aug 2020 10:24:29 -0500

ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG.

Address of the bookmark: http://www.ici.upmc.fr/cluego/

DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes

Rahul Nayak — Tue, 30 Mar 2021 11:47:29 -0500

Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology.

DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.

Address of the bookmark: http://www.essentialgene.org/

2.4 Mb Genome Size for World's Biggest Virus

Jitendra Narayan — Thu, 08 Aug 2013 10:05:37 -0500

The genome size of new discovered Pandoraviruses have roughly twice the size of the record-holding Megavirus genomic code. Interestingly only 6 percent of its genes resembled the genes other organisms. It is assume that it may come from a different origin.

For detail : http://www.sciencemag.org/content/341/6143/281

http://www.npr.org/blogs/health/2013/07/18/203298244/worlds-biggest-virus-may-have-ancient-roots