BOL: Related items

The ATCC Genome Portal

Abhi — Wed, 15 May 2024 14:24:16 -0500

The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC’s biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, we present new features and content added to the AGP for the research community.

Address of the bookmark: https://genomes.atcc.org/

Proksee

LEGE — Wed, 27 Mar 2024 11:11:54 -0500

Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

Please Cite the Following

Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C, Graham M, Van Domselaar G, and Stothard P

Proksee: in-depth characterization and visualization of bacterial genomes

Nucleic Acids Research, 2023, gkad326, https://doi.org/10.1093/nar/gkad326

Address of the bookmark: https://proksee.ca/

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

BioStar — Mon, 05 Aug 2024 23:01:29 -0500

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

Using state of the art tools, easily extended for other viruses
Tool and database updates for critical components via Conda
Built using modern design patterns with Conda and Snakemake
Extensible and easy to customize
Submission Ready Genomes
Customizable reporting with comprehensive visualization

https://ikim-essen.github.io/uncovar/

Github https://github.com/IKIM-Essen/uncovar

Address of the bookmark: https://ikim-essen.github.io/uncovar/

Early Genome Screening: The New Health Horoscope!

LEGE — Thu, 02 Jan 2025 19:44:36 -0600

In an era where precision medicine is reshaping healthcare, genome screening is emerging as the modern equivalent of a health horoscope. It offers insights into our biological "stars," unraveling predispositions to various conditions and empowering individuals with knowledge to navigate their health journeys proactively. But how reliable is this "horoscope," and how does it impact our lives?

Understanding Genome Screening

Genome screening involves analyzing an individual's DNA to identify genetic variations that may influence health and disease susceptibility. This can range from simple single-gene tests to comprehensive whole-genome sequencing. By peering into our genetic blueprint, we can uncover risks for conditions like cancer, diabetes, cardiovascular diseases, and even rare genetic disorders.

The process is straightforward: a saliva or blood sample is collected, and advanced sequencing technologies decipher the genetic code. The results provide a personalized health map, guiding lifestyle modifications, preventive measures, or medical interventions.

A Shift from Reactive to Proactive Healthcare

Traditional healthcare often focuses on treating diseases after they manifest. Genome screening flips this model on its head, enabling a shift toward prevention and early intervention. For instance:

Cancer Risk Management: Individuals with BRCA1 or BRCA2 gene mutations can opt for enhanced screening programs or preventive surgeries to mitigate their risk of breast and ovarian cancers.
Cardiovascular Health: Genetic predispositions to conditions like familial hypercholesterolemia can prompt early cholesterol monitoring and lifestyle adjustments.
Rare Diseases: Identifying carriers of genetic disorders can aid in family planning and reduce the incidence of inherited conditions.

The Ethical and Practical Concerns

While genome screening offers incredible promise, it is not without challenges:

Accuracy and Interpretation: Genetic predisposition does not guarantee disease. Misinterpretation of results can lead to unnecessary anxiety or unwarranted medical interventions.
Privacy and Data Security: Genetic data is highly sensitive. Ensuring robust data protection measures is crucial to prevent misuse.
Accessibility and Equity: High costs and limited availability may restrict access to genome screening, exacerbating health disparities.

Balancing Science and Pseudoscience

The comparison of genome screening to horoscopes isn’t entirely unfounded. Both offer predictive insights, but the scientific foundation of genome screening distinguishes it from astrology. Unlike the alignment of celestial bodies, genetic predictions are based on rigorous data and evidence. However, the probabilistic nature of genetic predispositions underscores the importance of interpreting results in conjunction with clinical and lifestyle factors.

The Road Ahead

As genome screening becomes more affordable and integrated into routine healthcare, its potential to transform lives is immense. Policymakers, healthcare providers, and genetic counselors must collaborate to ensure ethical implementation, public awareness, and equitable access.

Imagine a future where your genetic "horoscope" is a trusted guide, not just a prediction. Early genome screening could help chart a healthier path for generations, making it a cornerstone of personalized medicine. After all, our genes might just hold the key to unlocking a future of better health and well-being.

Introduction to programming. Write short programs that generate graphics and animation.

Ram Yash Pal — Thu, 14 Aug 2014 23:29:04 -0500

Introduction to programming. Write short programs that generate graphics and animation.

http://funprogramming.org/

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

Charpak exchange program

Fri, 10 Nov 2023 02:33:38 -0600

The scholarship is designed for Indian students from all fields and streams of study, enrolled in an Indian institution at the Bachelors or Master’s degree level, who wish to undertake a study exchange semester programme in France (for a period of one to six months).

BENEFITS
The Charpak exchange program offers the following benefits to the awardees based on merit: monthly stipend of 860 euros social security student visa and Campus France fee waiver assistance in finding an affordable student accommodation (subject to availability)

https://www.inde.campusfrance.org/charpak-exchange-scholarship-spring-session-jan-june

MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times

Poonam Mahapatra — Sat, 02 Jun 2018 07:40:06 -0500

MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy example modified from dataset of Inoue et al. (2010). Here we conduct a commonly used time estimation method, "Approximate Likelihood Method", for the datasets including more than 10 species.

Address of the bookmark: http://www.fish-evol.com/mcmctreeExampleVert6/text1Eng.html

CroCo: A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification

Jit — Mon, 07 Jan 2019 18:17:44 -0600

CroCo is a program to detect cross contamination events in assembled transcriptomes using sequencing reads to determine the true origin of every transcripts.
Such cross contaminations can be expected if several RNA-Seq experiments were prepared during the same period at the same lab, or by the same people, or if they were processed or sequenced by the same sequencing service facility.
Our approach first determines a subset of transcripts that are suspiciously similar across samples using a pairwise BLAST procedure. CroCo then combine all transcriptomes into a metatranscriptome and quantifies the "expression level" of all transcripts successively using every sample read data (e.g. several species sequenced by the same lab for a particular study) while allowing read multi-mappings.
Several mapping tools implemented in CroCo can be used to estimate expression level (default is RapMap).
This information is then used to categorize each transcript in the following 5 categories :

clean: the transcript origin is from the focal sample.

cross contamination: the transcript origin is from an alien sample of the same experiment.

dubious: expression levels are too close between focal and alien samples to determine the true origin of the transcript.

low coverage: expression levels are too low in all samples, thus hampering our procedure (which relies on differential expression) to confidently assign it to any category.

over expressed: expression levels are very high in at least 3 samples and CroCo will not try to categorize it. Indeed, such a pattern does not correspond to expectations for cross contaminations, but often reflect highly conserved genes such as ribosomal gene, or external contamination shared by several samples (e.g. Escherichia coli contaminations).

Address of the bookmark: https://gitlab.mbb.univ-montp2.fr/mbb/CroCo

Gooey: Turn (almost) any Python command line program into a full GUI application with one line

BioStar — Fri, 01 Nov 2019 00:29:27 -0500

Turn (almost) any Python command line program into a full GUI application with one line

The easiest way to install Gooey is via pip

pip install Gooey

Alternatively, you can install Gooey by cloning the project to your local directory

git clone https://github.com/chriskiehl/Gooey.git

run setup.py

python setup.py install

Address of the bookmark: https://github.com/chriskiehl/Gooey