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3D-GENOMICS -- A Database to Compare Structural and Functional Annotations of Proteins between Sequenced Genomes
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| Compare structural and functional annotations of proteins between sequenced genomes.
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ACMES -- A fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval
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| Search for short repeats of DNA sequence of length between 3 and 10000 bases within multiple species.
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AnimalQTLdb -- a livestock QTL database tool set for positional QTL information mining and beyond
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| Search for publicly available QTL data on livestocks and animal species. |
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CGAS -- a comparative genome annotation system
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| A web-based genome annotation system.
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COMPARE -- a multi-organism system for cross-species data comparison and transfer of information
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| A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.
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CONDOR -- COnserved Non-coDing Orthologous Regions
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| A database resource of developmentally associated conserved non-coding elements.
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CORG -- A database for COmparative Regulatory Genomics
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| Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish. |
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CVTree -- A Phylogenetic Tree Reconstruction Tool Based on Whole Genomes
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| Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.
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CleanEST -- the cleansed EST libraries database
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| A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.
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Comparative Genometrics (CG) -- a database dedicated to biometric comparisons of whole genomes
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| Conduct comparative biometric analysis of chromosomes of different organisms. |
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DoTS -- Database Of Transcribed Sequences
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| Search for Indices of gene and transcripts in human and mouse.
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DroSpeGe -- rapid access database for new Drosophila species genomes
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| Search and compare 12 new and old Drosophila genomes. |
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ECR Browser -- A Tool for Visualizing and Accessing Data from Comparisons of Multiple Vertebrate Genomes
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| Access to whole genome alignments of human, mouse, rat and fish sequences.
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EPGD -- Eukaryotic Paralog Group Database
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| Find eukaryotic paralog/paralogon information.
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EVOG -- evolutionary visualizer for overlapping genes
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| Analyze the evolutionary process of overlapping genes when comparing different species.
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ExDom -- Exon-Intron structures of protein domains database
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| Analyze exon-intron structures of protein domains in eukaryotes.
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GenColors -- annotation and comparative genomics of prokaryotes made easy
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| A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.
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GeneNest gene indices
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| Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.
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GeneSyn -- a tool for detecting conserved gene order across genomes
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| Conduct automatic detection of conserved gene order from annotated genomes.
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GeneTrees -- a phylogenomics resource for prokaryotes
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| Search for pre-computed alignments and phylogenetic trees for all protein sequences from 325 fully sequenced and annotated prokaryote genomes.
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GenomeTrafac -- a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
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| Use comparative genomics approach to characterize gene models and identify putative cis-regulatory regions of RefSeq Gene Orthologs.
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MANTIS -- a phylogenetic framework for multi-species genome comparisons
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| The missing link between multi-species full genome comparisons and functional analysis.
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MBGD -- Microbial genome database for comparative analysis
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| Conduct comparative analysis of completely sequenced microbial genomes. |
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MEGA -- Molecular Evolutionary Genetics Analysis
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| A biologist-centric software for evolutionary analysis of DNA and protein sequences.
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MamPol -- a database of nucleotide polymorphism in the Mammalia class
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| Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class. |
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MultiPhyl -- A high-throughput phylogenomics webserver using distributed computing
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| Upload multiple amino acid or nucleotide alignments and perform the tasks of ML model selection, tree searching, and bootstrapping. |
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Narcisse -- a mirror view of conserved syntenies
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| A database dedicated to the study of genome conservation.
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OMA -- the Orthologous MAtrix project
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| Explore orthologous relations across 352 complete genomes.
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OPTIC -- orthologous and paralogous transcripts in clades
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| Browse complete genomes in several clades.
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OrthoMaM -- orthologous mammalian markers
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| A database of orthologous genomic markers for placental mammal phylogenetics.
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PEDANT -- Protein Extraction, Description and ANalysis Tool
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| Conduct genome wide functional and structural analysis. |
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PReMod -- a database of genome-wide mammalian cis-regulatory module predictions
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| Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes. |
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PUMA2 — grid-based high-throughput analysis of genomes and metabolic pathways
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| Carry out high-throughput genetic sequence analysis and metabolic reconstructions from sequence data. |
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PhenomicDB -- Comparison of phenotypes of orthologous genes in human and model organisms
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| Compare phenotypes of a given gene or gene set in different model organisms.
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Phylemon -- A suite of web tools for molecular evolution, phylogenetics and phylogenomics
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| Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis. |
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PhyloPat -- the phylogenetic pattern database
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| Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.
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Pristionchus.org -- a genome-centric database of the nematode satellite species Pristionchus pacificus
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| Search for genomic information on nematode satellite species Pristionchus pacificus. |
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Pseudofam -- the pseudogene families database
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| A database of pseudogene families based on the protein families from the Pfam database.
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SGN -- SOL Genomics Network
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| A comparative map viewer dedicated to the biology of the Solanaceae family.
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SwissRegulon -- a database of genome-wide annotations of regulatory sites
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| Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes. |
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TaxonGap -- a visualization tool for intra- and inter-species variation among individual biomarkers
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| Compare and select individual biomarkers.
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The Adaptive Evolution Database (TAED) -- a phylogeny based tool for comparative genomics
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| Search for information on adaptive evolution in gene families of higher plants and chordate. |
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The CGView Server -- a comparative genomics tool for circular genomes
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| Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.
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The ERGO -- Genome analysis and discovery system
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| Conduct a comprehensive analysis of genes and genomes.
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The Macaque Genome: Interactive Poster and Teaching Resource
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| An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources
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The TIGR Gene Indices -- clustering and assembling EST and known genes and integration with eukaryotic genomes
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| Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms. |
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UniGene
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| Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene) |
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Uprobe -- universal overgo hybridization-based probe retrieval and design
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| A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.
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VISTA -- Computational Tools for Comparative Genomics
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| Comprehensive suite of programs and databases for comparative analysis of genomic sequences.
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xBASE -- a collection of online databases for bacterial comparative genomics
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| Conduct bacterial comparative genomics.
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