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Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name.
Proper citation: Maize Database of Images and Genomes (RRID:SCR_016987) Copy
https://github.com/Rinoahu/SwiftOrtho
Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.
Proper citation: SwiftOrtho (RRID:SCR_017122) Copy
https://github.com/im3sanger/dndscv
Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets.
Proper citation: dndSCV (RRID:SCR_017093) Copy
https://github.com/josephryan/matemaker
Software tool to make artificial mate pairs from long sequences for scaffolding.
Proper citation: matemaker (RRID:SCR_017199) Copy
http://www.cbs.dtu.dk/services/RNAmmer/
Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.
Proper citation: RNAmmer (RRID:SCR_017075) Copy
http://www-sequence.stanford.edu/group/candida/
The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects.
Proper citation: Sequencing of Candida Albicans (RRID:SCR_013437) Copy
Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6.
Proper citation: PiGenome (RRID:SCR_013394) Copy
http://bioinformatics.psb.ugent.be/ENIGMA/
A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007
Proper citation: ENIGMA (RRID:SCR_013400) Copy
http://fnih.org/work/past-programs/genetic-association-information-network-gain
The Genetic Association Information Network (GAIN) supports a series of Genome-Wide Association Studies (GWAS) designed to identify specific points of DNA variation associated with the occurrence of a particular common disease. Initially focusing on six major common diseases, GAIN focused on combining the results with clinical data to create a significant new resource for genetic researchers.
Proper citation: Genetic Association Information Network (GAIN) (RRID:SCR_013703) Copy
http://www.vicbioinformatics.com/software.prokka.shtml
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Prokka (RRID:SCR_014732) Copy
https://www.encodeproject.org/
Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present.
Proper citation: Encode (RRID:SCR_015482) Copy
http://www.vicbioinformatics.com/software.barrnap.shtml
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Barrnap (RRID:SCR_015995) Copy
Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.
Proper citation: BECA (RRID:SCR_015846) Copy
http://standage.github.io/AEGeAn
Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.
Proper citation: Aegean (RRID:SCR_015965) Copy
http://www.alliancegenome.org/
Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN).
Proper citation: Alliance of Genome Resources (RRID:SCR_015850) Copy
https://github.com/EvolBioInf/andi
Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.
Proper citation: andi (RRID:SCR_015971) Copy
https://github.com/thackl/cross-species-scaffolding
Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references.
Proper citation: Cross-species scaffolding (RRID:SCR_015932) Copy
https://github.com/harry-thorpe/piggy
Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).
Proper citation: Piggy (RRID:SCR_015941) Copy
Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways.
Proper citation: MetaNetX (RRID:SCR_015882) Copy
http://bejerano.stanford.edu/phenotree/
Web server to search for genes involved in given phenotypic difference between mammalian species. The mouse-referenced multiple alignment data files used to perform the forward genomics screen is also available. The webserver implements one strategy of a Forward Genomics approach aiming at matching phenotype to genotype. Forward genomics matches a given pattern of phenotypic differences between species to genomic differences using a genome-wide screen. In the implementation, the divergence of the coding region of genes in mammals is measured. Given an ancestral phenotypic trait that is lost in independent mammalian lineages, it is shown that searching for genes that are more diverged in all trait-loss species can discover genes that are involved in the given phenotype.
Proper citation: Phenotree (RRID:SCR_003591) Copy
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