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JGI Genome Portal logoJGI publishes all its sequenced genomes on its Genome Portal. Here you can download sequence files, BLAST against a particular genome, and view annotations. Advanced tools, including genome, GO, KEGG, and KOG browsers, are available for eukaryotes. JGI's Genome Browser lets you browse through JGI-predicted genes, view sequences, and study detailed alignments with nucleotide and amino acid sequences from relevant sequence databases.

JGI Mycocosm thumb The JGI Mycocosm web-portal provides data access, visualization, and analysis tools for comparative genomics of fungi. Mycocosm enables users to navigate across sequenced fungal genomes, and to conduct comparative and genome-centric analyses of fungi and community annotation. 		The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life, in a uniquely integrated context. IMG with Microbiome Samples (IMG/M) provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence, in the context of reference isolate genomes included from the IMG system. IMG Education Site (IMG/EDU) provides training and teaching support for genome analysis applied to the annotation of microbial genomes. IMG Expert Review (IMG/ER) provides support to individual scientists or groups of scientists for functional annotation and curation of microbial genomes of interest, usually prior to their release to Genbank. Additionally, IMG with Microbiome Samples Expert Review (IMG/M-ER), and IMG for the Human Microbiome Project (IMG-HMP).
VISTAVISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. Group lead, Inna Dubchak The Phytozome project organizes the proteomes of green plants into gene families defined at nodes on the green plant evolutionary tree. You can study the evolutionary history of a gene of interest from one of the included proteomes or place a gene from a different plant in the most appropriate gene family. Alternatively, you can BLAST search and browse the genomes of any of the included green plants. Phytozome makes it easy to move back and forth between organism-centric and gene family-centric views.
GENEPRIMPGenePRIMP (Gene PRediction IMprovement Pipeline) is a pipeline that consists of a series of computational units that identify erroneous gene calls and missed genes and correct a subset of the identified defective features. The input to GenePRIMP needs to be a file of gene calls in GenBank or EMBL format. As its output, GenePRIMP generates reports of identified gene prediction anomalies. FAMESFAMeS provides access to simulated datasets and aims to facilitate standardized benchmarking of tools for metagenomic analysis. To evaluate methods currently used to process metagenomic sequences, simulated datasets of varying complexity were constructed by combining sequencing reads randomly selected from 113 isolate genomes. These datasets were designed to model real metagenomes in terms of complexity and phylogenetic composition.
"Gap Resolution" software (available for academic use): Gap Resolution was developed by DOE Joint Genome Institute to improve Newbler genome assemblies by automating the closure of sequence gaps caused by repetitive regions in the DNA. If you are interested in acquiring this software, please contact degilbert@lbl.gov

For more information, download the poster.		 "Polisher" (available for academic use): Polisher is a software package designed to facilitate the error correction of an assembled genome using Illumina read data by automatically correcting consensus errors and/or suggesting primer walking reactions to improve the base quality. If you are interested in acquiring this software, please contact degilbert@lbl.gov

For more information, download the poster.
"Rnnotator" software: To address challenges related to comprehensive annotation and quantification of transcriptomes, Rnnotator was developed by a team at the JGI to provide an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome.  It is freely available to academic users by request:  degilbert@lbl.gov