About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.ympev.2012.08.023 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Automated stenosis estimation of coronary angiographies using end-to-end learning.
Int J Cardiovasc Imaging
January 2025
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
The initial evaluation of stenosis during coronary angiography is typically performed by visual assessment. Visual assessment has limited accuracy compared to fractional flow reserve and quantitative coronary angiography, which are more time-consuming and costly. Applying deep learning might yield a faster and more accurate stenosis assessment.
View Article and Find Full Text PDFPTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways.
Nat Commun
January 2025
Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany.
Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level. Here, we present PTMNavigator, a tool integrated into the ProteomicsDB platform that offers an interactive interface for researchers to overlay experimental PTM data with pathway diagrams.
View Article and Find Full Text PDFAssessing Artificial Intelligence (AI) Implementation for Assisting Gene Linking (at the National Library of Medicine).
JAMIA Open
February 2025
National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States.
Objectives: The National Library of Medicine (NLM) currently indexes close to a million articles each year pertaining to more than 5300 medicine and life sciences journals. Of these, a significant number of articles contain critical information about the structure, genetics, and function of genes and proteins in normal and disease states. These articles are identified by the NLM curators, and a manual link is created between these articles and the corresponding gene records at the NCBI Gene database.
View Article and Find Full Text PDFMalay translation and validation of modified checklist for autism in toddlers, revised with follow-up (M-CHAT-R/F).
Front Pediatr
December 2024
Child Development Centre (CDC), Department of Pediatrics, Universiti Kebangsaan Malaysia Medical Centre (UKMMC), Kuala Lumpur, Malaysia.
Introduction: Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition diagnosed clinically based on phenotypic characteristics and criteria such as the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). Due to its significant social, emotional, and psychological impacts, early identification and diagnosis are crucial for starting early intervention and improving outcomes. A screening tool is imperative in identifying young children at risk so timely intervention can be instituted.
View Article and Find Full Text PDFThe anti-MRSA resource: a comprehensive archive of anti-MRSA peptides and essential oils.
J Biomol Struct Dyn
January 2025
Biochemistry and Bioinformatics Laboratory, Department of Applied Sciences, Indian Institute of Information Technology Allahabad (IIIT-A), Prayagraj, Uttar Pradesh, India.
Methicillin-resistant (MRSA), a major cause of fatalities due to Antimicrobial Resistance (AMR), can act as an opportunistic pathogen despite being part of the normal human flora. MRSA infections, such as skin infections, pneumonia, sepsis, and surgical site infections, have risen significantly, with bloodstream infection cases increasing from 21% in 2016 to 35% in 2020. This surge has prompted research into alternative treatments like nanomaterials, photodynamic therapy, antimicrobial peptides (AMPs), and essential oils (EOs).
View Article and Find Full Text PDFWant 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!