Search
Search Results
-
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent...
-
Pangenome graph construction from genome alignments with Minigraph-Cactus
Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a...
-
Comparative Genome Annotation
Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. A large proportion of such new genomes are...
-
De-MISTED: Image-based classification of erroneous multiple sequence alignments using convolutional neural networks
The widespread use of high throughput genome sequencing technologies has resulted in a significant increase in the number of available sequences,...
-
SALON ontology for the formal description of sequence alignments
BackgroundInformation provided by high-throughput sequencing platforms allows the collection of content-rich data about biological sequences and...
-
EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
BackgroundAdding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with...
-
Improvements in viral gene annotation using large language models and soft alignments
BackgroundThe annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute...
-
Technologies Promoting Genome-Based Taxonomy
Whole-genome sequencing (WGS) has proven to be a reliable method. Additionally, it is a commonly used approach in research and surveillance...
-
The arithmetic topology of genetic alignments
We propose a novel mathematical paradigm for the study of genetic variation in sequence alignments. This framework originates from extending the...
-
SAM: cross-modal semantic alignments module for image-text retrieval
Cross-modal image-text retrieval has gained increasing attention due to its ability to combine computer vision with natural language processing....
-
Family-Free Genome Comparison
The comparison of large-scale genome structures across distinct species offers valuable insights into the species’ phylogeny, genome organization,...
-
Phased Genome Assemblies
The ultimate goal of de novo assembly of reads sequenced from a diploid individual is the separate reconstruction of the sequences corresponding to...
-
Crucifer’s Pathogens Genome
The information on genome sequences, analysis and assembly of limited pathogens of crucifers has been generated and made available. It has given...
-
Structural and Functional Annotation of the Wheat Genome
Wheat genome sequencing has passed through major steps in a decade, starting from the sequencing of large contiguous sequences obtained from...
-
Scaling up multiple-genome alignments
Progressive Cactus enables reference-free multiple-genome alignment for massive datasets.
-
Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management
BackgroundWhile recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of...
-
Step-by-Step Bacterial Genome Comparison
Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This...
-
Multiple genome alignment in the telomere-to-telomere assembly era
With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately...
-
Improved sequence map** using a complete reference genome and lift-over
Complete, telomere-to-telomere (T2T) genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic...
-
The Bread Wheat Reference Genome Sequence
In 2018, the International Wheat Genome Sequencing Consortium published a reference genome sequence for bread wheat (Triticum aestivum L.). The...