SPEAR: Systematic ProtEin AnnotatoR.

Bioinformatics

Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.

Published: August 2022

Summary: We present Systematic ProtEin AnnotatoR (SPEAR), a lightweight and rapid SARS-CoV-2 variant annotation and scoring tool, for identifying mutations contributing to potential immune escape and transmissibility (ACE2 binding) at point of sequencing. SPEAR can be used in the field to evaluate genomic surveillance results in real time and features a powerful interactive data visualization report.

Availability And Implementation: SPEAR and documentation are freely available on GitHub: https://github.com/m-crown/SPEAR and are implemented in Python and installable via Conda environment.

Supplementary Information: Supplementary data are available at Bioinformatics online.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9344845PMC
http://dx.doi.org/10.1093/bioinformatics/btac391DOI Listing

Publication Analysis

Top Keywords

systematic protein
8
protein annotator
8
spear
4
spear systematic
4
annotator summary
4
summary systematic
4
annotator spear
4
spear lightweight
4
lightweight rapid
4
rapid sars-cov-2
4

Similar Publications

Background: Cytokeratins are intracellular proteins known as diagnostic biomarkers or prognostic factors for certain cancers. Cytokeratin 19 (CK-19) expression has been proven to have prognostic value for some cancers, but its relationship with others, such as prostate cancer (PCa), remains unclear. This systematic review article aimed to examine the relationship between CK-19 expression and prostate adenocarcinoma (PAC).

View Article and Find Full Text PDF

This study aims to elucidate the potential genetic commonalities between metabolic syndrome (MetS) and rheumatic diseases through a disease interactome network, according to publicly available large-scale genome-wide association studies (GWAS). The analysis included linkage disequilibrium score regression analysis, cross trait meta-analysis and colocalisation analysis to identify common genetic overlap. Using modular partitioning, the network-based association between the two disease proteins in the protein-protein interaction set was divided and quantified.

View Article and Find Full Text PDF

Capturing eukaryotic ribosome dynamics in situ at high resolution.

Nat Struct Mol Biol

January 2025

Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ribosome particles from Saccharomyces cerevisiae cell lamellae were obtained to solve the 60S region to 2.9-Å resolution by in situ single-particle analysis.

View Article and Find Full Text PDF

Lactic acid bacteria (LAB), traditionally consumed as fermented foods, are now being applied to the medical field beyond health-functional food as probiotics. Therefore, it is necessary to continuously discover and evaluate new strains with suitable probiotic characteristics, mainly focusing on safety. In this study, we isolated eight new strains from postmenopausal vaginal fluid using culturomics approaches, an emerging area of interest.

View Article and Find Full Text PDF

Pugionium cornutum (L.) Gaertn (P. cornutum) has strong tolerance to drought, salt and disease, but the tolerance mechanisms for such stresses in P.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!