bioinformatics | Ag Data Commons

Data from: Use of long-read sequencing simulators to assess real-world applications for food safety

The goal of this project was to use NanoSim-H software to simulate Oxford Nanopore sequencing reads to assess the feasibility of sequencing-based foodborne pathogen detection and guide experimental design. Sequencing reads were simulated for STEC, *L. monocytogenes*, and a 1:1 combination of STEC and *Bos taurus* genomes using NanoSim-H. This dataset includes all of the simulated reads generated by the project in fasta format.

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Data from: Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to PRRSV infection. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with PRRSV.

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Bradysia coprophila genome annotations Bcop_v1.0

This dataset presents the Bradysia coprophila genome annotations Bcop_v1.0. It will be used as a starting point to manually improve annotations.

Long-term Crop Rotation Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Lubbock, Texas

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Breedbase

The Breedbase system has evolved from the Sol Genomics Network (SGN) and Cassavabase and related sites (see RTBbase.org).Breedbase is striving to be a complete breeding management system, including field management, data collection, crossing utilities, and advanced trial analysis.

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CottonGen Synteny Viewer

View synteny among Cotton genomes using the new Tripal Synteny Viewer

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WheatIS

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

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Sol Genomics Network (SGN)

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Variants from "The role of deleterious substitutions in crop genomes"

SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.

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BAR- The Bio-Analytic Resource for Plant Biology

BAR is a collection of web-based, user-friendly tools for exploring, visualizing, and analyzing large datasets from plants. Supported are expression data, Next-Gen sequence data, protein-protein interactions, polymorphisms / conservation, and protein 3-D structures.

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