Alan Cleary

The SoyBase, LegumeInfo, and PeanutBase databases in support of legume research and crop improvement

J. Todd Campbell, Connor Cameron, Alan Cleary, Sudhansu Dash et autres

Here, we describe a collection of genomic database portals, SoyBase (https://soybase.org), Legume Information System (https://legumeinfo.org), and PeanutBase (https://peanutbase.org), that support breeding and research work in the legume plant family. The legume family includes important crops such as soybean, peanut, common bean, lentils, …

us (code pays fourni par la source)

Revisiting the Folklore Algorithm for Random Access to Grammar-Compressed Strings

Alan Cleary, Joseph Winjum, Jordan Dood, Shunsuke Inenaga

us, jp (code pays fourni par la source)

Revisiting the Folklore Algorithm for Random Access to Grammar-Compressed Strings

Alan Cleary, Joseph Winjum, Jordan Dood, Shunsuke Inenaga

Grammar-based compression is a widely-accepted model of string compression that allows for efficient and direct manipulations on the compressed data. Most, if not all, such manipulations rely on the primitive \emph{random access} queries, a task of quickly returning the character at a …

The CDAWG Index and Pattern Matching on Grammar-Compressed Strings

Alan Cleary, Joseph Winjum, Jordan Dood, Shunsuke Inenaga

The compact directed acyclic word graph (CDAWG) is the minimal compact automaton that recognizes all the suffixes of a string. Classically the CDAWG has been implemented as an index of the string it recognizes, requiring $o(n)$ space for a copy of the …

Genotype-to-Phenotype Associations with Frequented Region Variants

Indika Kahanda, Buwani Manuweera, Brendan Mumey, Thiruvarangan Ramaraj et autres

A pangenome represents the entire sequence content and variation of a population. As collections of complete reference quality genomes become more common, so does the prevalence of pangenomes, necessitating the need for scalable computational methods for their analysis. Previously, we developed FindFRs …

us (code pays fourni par la source)

Graph-Based Machine Learning Approaches for Pangenomics

Indika Kahanda, Joann Mudge, Buwani Manuweera, Thiruvarangan Ramaraj et autres

us (code pays fourni par la source)

Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes

Alan Cleary, Andrew Farmer

The Genome Context Viewer is a web application for identifying, aligning, and visualizing genomic regions based on their micro and macrosyntenic structures. By using functional elements such as gene annotations as the unit of search and comparison, the Genome Context Viewer can …

us (code pays fourni par la source)

Constructing the CDAWG CFG using LCP-Intervals

Alan Cleary, Jordan Dood

It is known that a context-free grammar (CFG) that produces a single string can be derived from the compact directed acyclic word graph (CDAWG) for the same string. In this work, we show that the CFG derived from a CDAWG is deeply …

us (code pays fourni par la source)

Ten simple rules for developing visualization tools in genomics

Éloi Durant, Mathieu Rouard, Eric Ganko, Cedric Muller et autres

Visualization is key for expanding and communicating knowledge to both specialized and broad audiences-after all, "a picture is worth a thousand words," right?That much has become clear during the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak when "Flatten the curve!" [1] …

fr, in, us (code pays fourni par la source)

Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources

Sven Redsun, Sam Hokin, Connor Cameron, Alan Cleary et autres

us (code pays fourni par la source)

A strategy for building and using a human reference pangenome

Bastien Llamas, Giuseppe Narzisi, Valérie Schneider, Peter A. Audano et autres

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome …

au, us, de, jp (code pays fourni par la source)

SnpReportR: A Tool for Clinical Reporting of RNAseq Expression and Variants

Ahmad Al Khleifat, Jenny L. Smith, Brandon M. Blobner, Sierra Miller et autres

With the increasing availability of next-generation sequencing (NGS), patients and non-specialist health care professionals are obtaining their genomic information without sufficient bioinformatics skills to analyze and interpret the data. In January 2021, four teams of scientists,clinicians, and developers from around the world …

us, Nigéria, ch (code pays fourni par la source)