<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39903?offset=170 https://bioinformaticsonline.com/bookmarks/view/43690/ucsc-sars-cov-2-genome-browser Thu, 06 Jan 2022 06:48:40 -0600 https://bioinformaticsonline.com/bookmarks/view/43690/ucsc-sars-cov-2-genome-browser <![CDATA[UCSC SARS-CoV-2 Genome Browser]]> The UCSC SARS-CoV-2 Genome Browser (https://genome.ucsc.edu/covid19.html) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT–PCR and sequencing primers and CRISPR guides. We invite all investigators to contribute to this resource to accelerate research and development activities globally.

Address of the bookmark: https://www.nature.com/articles/s41588-020-0700-8

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43859/mumco-is-a-simple-bash-script-that-uses-whole-genome-alignment-information-provided-by-mummer-v4-to-detect-variants Wed, 27 Apr 2022 04:34:12 -0500 https://bioinformaticsonline.com/bookmarks/view/43859/mumco-is-a-simple-bash-script-that-uses-whole-genome-alignment-information-provided-by-mummer-v4-to-detect-variants <![CDATA[MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v4) to detect variants.]]> MUM&Co is able to detect:
Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)
Inversions (>=1kb) and translocations (>=10kb)

Address of the bookmark: https://github.com/SAMtoBAM/MUMandCo

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/44537/the-atcc-genome-portal Wed, 15 May 2024 14:24:16 -0500 https://bioinformaticsonline.com/bookmarks/view/44537/the-atcc-genome-portal <![CDATA[The ATCC Genome Portal]]> 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/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44489/proksee Wed, 27 Mar 2024 11:11:54 -0500 https://bioinformaticsonline.com/bookmarks/view/44489/proksee <![CDATA[Proksee]]> 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
Nucleic Acids Research, 2023, gkad326, https://doi.org/10.1093/nar/gkad326

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

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/44628/uncovar-workflow-for-transparent-and-robust-virus-variant-calling-genome-reconstruction-and-lineage-assignment Mon, 05 Aug 2024 23:01:29 -0500 https://bioinformaticsonline.com/bookmarks/view/44628/uncovar-workflow-for-transparent-and-robust-virus-variant-calling-genome-reconstruction-and-lineage-assignment <![CDATA[UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment]]> 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/

]]> BioStar https://bioinformaticsonline.com/blog/view/44754/early-genome-screening-the-new-health-horoscope Thu, 02 Jan 2025 19:44:36 -0600 https://bioinformaticsonline.com/blog/view/44754/early-genome-screening-the-new-health-horoscope <![CDATA[Early Genome Screening: The New Health Horoscope!]]> 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:

  1. Accuracy and Interpretation: Genetic predisposition does not guarantee disease. Misinterpretation of results can lead to unnecessary anxiety or unwarranted medical interventions.

  2. Privacy and Data Security: Genetic data is highly sensitive. Ensuring robust data protection measures is crucial to prevent misuse.

  3. 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.

 

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/38908/busca-an-integrative-web-server-to-predict-subcellular-localization-of-proteins Thu, 07 Feb 2019 14:08:11 -0600 https://bioinformaticsonline.com/bookmarks/view/38908/busca-an-integrative-web-server-to-predict-subcellular-localization-of-proteins <![CDATA[BUSCA: an integrative web server to predict subcellular localization of proteins]]> BUSCA (Bologna Unified Subcellular Component Annotator) is a web-server for predicting protein subcellular localization. BUSCA integrates different tools to predict localization-related protein features (DeepSig, TPpred3, PredGPI and ENSEMBLE3.0) as well as tools for discriminating subcellular localization of both globular and membrane proteins (BaCelLo, MemLoci and SChloro).

Address of the bookmark: http://busca.biocomp.unibo.it/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/34404/sima-c-implementation-simultaneous-multiple-alignment-of-lcms-peak-lists Thu, 23 Nov 2017 17:15:52 -0600 https://bioinformaticsonline.com/bookmarks/view/34404/sima-c-implementation-simultaneous-multiple-alignment-of-lcms-peak-lists <![CDATA[SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists]]> This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit, Windows Vista 32bit, Windows 2008 Server, Windows 7 32bit and 64bit, Ubuntu 10.04 64bit, Ubuntu 10.10 64bit, and gentoo AMD64.

The corresponding publication can be found here:

B. Voss*, M. Hanselmann*, B.Y. Renard, M.S. Lindner, U. Köthe, M. Kirchner, F.A. Hamprecht (2011). SIMA: Simultaneous Muliple Alignment of LC/MS Peak Lists, Bioinformatics 27(7):987-993. [doi] [techreport]

Address of the bookmark: https://hciweb.iwr.uni-heidelberg.de/hci/softwares/sima

]]> Neel https://bioinformaticsonline.com/bookmarks/view/36800/genomemapper-simultaneous-alignment-of-short-reads-against-multiple-genomes Fri, 25 May 2018 09:29:44 -0500 https://bioinformaticsonline.com/bookmarks/view/36800/genomemapper-simultaneous-alignment-of-short-reads-against-multiple-genomes <![CDATA[GenomeMapper: Simultaneous alignment of short reads against multiple genomes]]> Address of the bookmark: http://1001genomes.org/software/genomemapper.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences Fri, 01 Nov 2019 00:20:41 -0500 https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences <![CDATA[Kalign: fast multiple sequence alignment program for biological sequences.]]> Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

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