همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

Orthology inference at scale with FastOMA

نویسندگان :

Sina Majidian¹ Yannis Nevers² Ali Yazdizadeh Kharrazi³ Christophe Dessimoz⁴

1- John Hopkins University 2- University of Lausanne 3- University of Tehran 4- University of Lausanne

کلمات کلیدی :

Orthology،k-mers،Comparative Genomics

چکیده :

The unprecedented increase in genomic data, fueled by initiatives such as the Earth BioGenome Project, which aims to sequence 1.5 million eukaryotic genomes, holds immense potential to advance our understanding of evolution and biological diversity. However, traditional orthology inference methods, which identify genes of common ancestry across species, struggle to process datasets at this scale. We present FastOMA, a novel orthology inference tool that scales linearly with input size, enabling the analysis of thousands of genomes in under 24 hours with minimal computational resources. By combining k-mer-based clustering, taxonomy-guided subsampling, and efficient parallelization, FastOMA maintains high accuracy and recall, outperforming established orthology methods in benchmarks. FastOMA demonstrates remarkable precision on the Quest for Orthologs and SwissTree benchmarks and achieves low topological error in species tree comparisons, establishing it as a state-of-the-art solution for large-scale orthology inference. The tool’s flexibility with taxonomic inputs, robustness to phylogenetic errors, and compatibility with the OMA ecosystem provide an essential resource for researchers aiming to explore evolutionary patterns at unprecedented scales. FastOMA is available at https://github.com/DessimozLab/FastOMA/.

لیست مقالات

لیست مقالات بایگانی شده

Upregulation of IL6 as a Hub Gene in Metastatic Breast Cancer: Insights from Gene Expression and Network Analysis

Roxana Tajdini - Farinaz Behfarjam - Maryam Shahhoseini - Mostafa Rafiepour

Bioinformatics Analysis of Prostate Cancer by the Construction of circRNA-miRNA-mRNA Regulatory Network

Fatemeh Zamani - Ali Taravati

Solving Diffusion Equations Using Physics-Informed Neural Networks: A Biological Application

Yasaman Razzaghi - Ali Shokri - Ahmad Aliyari Boroujeni

Drug repurposing using bulk RNA-seq based on key genes involved in inflammatory bowel disease

Nayereh Abdali - Shahram Tahmasebian - Atena Vaghf

Investigation and comparison of TYDC2 gene expression in different tissues (root, leaf, capsule and petal) of medicinal plant poppy (Papaver somniferum L.) in terms of bioinformatics

Nazila Bagheri - Alireza Tarinejad - Mohammad Majidi - Karim Hasanpour

Identifying mRNAs and miRNAs in extracellular vesicles through comparative transcriptome analyses of healthy and mastitic bovine milk

Farzad Ghafouri - Seyed Midia Pirkhezranian - Mostafa Sadeghi - Seyed Reza Miraei-Ashtiani - John P. Kastelic - Herman W. Barkema - Vahid Razban - Masoud Shirali

Astrocyte-Mediated Regulation of Neurogenesis in the Anterior Hippocampus of Alzheimer's Disease Patients

Sarvenaz Sahebekhtiari - Morteza Hadizadeh - Hamid Forootanfar - Masoud Rezaei - Alieh Ameri - Mojtaba Shakibaie

Machine Learning for Enhanced Diagnosis of Endometriosis: Challenges and Opportunities

Maedeh Darodi - Toktam Dehghani

Molecular Investigation of Periplasmic Sensor Histidine Kinase Interactions in Regulating UV Shield Formation of Cyanobacteria Nostoc Sp

Maryam Eskafi - Maryam Azimzadeh Irani

In Silico Design of DNA G-Quadruplex Aptamers Targeting Lipopolysaccharide Core and Capsular Polysaccharide in Multidrug-Resistant Klebsiella pneumoniae

Aida Arezoumandchafi - Maryam Azimzadeh Irani - Hamidreza Mollasalehi

بیشتر

ثمین همایش، سامانه مدیریت کنفرانس ها و جشنواره ها - نگارش 42.7.0