Quick access to genome database and software.
Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere.
Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data.
The Genome Warehouse (GWH) is a public repository housing genome-scale data for a wide range of species and delivering a series of web services for genome data submission, storage, release and sharing.
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
CoGe is a platform for performing Comparative Genomics research. It provides an open-ended network of interconnected tools to manage, analyze, and visualize next-gen data.
GigaDB contains 2349 discoverable, trackable, and citable datasets that have been assigned DOIs and are available for public download and use.
PLAZA is a platform for comparative, evolutionary, and functional plant genomics.
Plant GARDEN (Genome And Resource Database Entry) is a portal sitethat curates genome and marker information of various plant species.
ORCAE is an online genome annotation resource offering users the necessary tools and information to validate and correct gene annotations.
The TreeGenes database provides custom informatics tools to manage the flood of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis.
The Genome Database for Rosaceae is a curated and integrated web-based relational database providing data mining tools and publicly available genomics, genetics and breeding data for Rosaceae (almond, apple, blackberry, cherry, peach, pear, plum, raspberry, rose, and strawberry), to aid basic, translational and applied research in this economically important family.
Solanaceae Genomics Network
A central portal for comparative and functional genomics of cucurbit crops
A Catalog of Arabidopsis thaliana Genetic Variation.
Pubished Plant Genomes
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50.
DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.
The DupGen_finder was developed to identify different modes of duplicated gene pairs.
EggNOG-mapper is a tool for fast functional annotation of novel sequences.
The Genome Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services.
GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more.
iTAK is a program to identify plant transcription factors (TFs), transcriptional regulators (TRs) and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs and PKs into different gene families.
JBrowse is a new kind of genome browser that runs on the web, on your desktop, or embedded in your app.
This software is a toolkit of incorporating gamma series methods and sliding window strategies.
a multiple sequence alignment program
The MCScanX package has two major components: a modified version of MCscan algorithm allowing users to handle MCScan more conveniently and to view multiple alignment of syntenic blocks more clearly, and a variety of downstream analysis tools to conduct different biological analyses based on the synteny data generated by the modified MCScan algorithm.
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics.
Our mission is to provide a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them, advancing the understanding of plant transcriptional regulatory system.
SHOOT is a phylogenetic alternative to BLAST.
An Interactive Multiscale Synteny Visualization Tool for McScanX.