| Bioinformatics (155) | This category contains links to resources relating to bioinformatics including DNA, RNA, sequence analysis, proteomics, and expression data. |
| Programming Portals (13) | |
| MySQL | |
| PostgreSQL | |
| Unix Home | |
| Free BSD | |
| Perl Home | |
| Perl Central Directory for All things Perl | |
| CPAN (Comprehensive Perl Archive Network) | |
| CPAN Search Index of Perl Modules: | |
| PHP Home | |
| Oracle Home | |
| MySQL Home | |
| SQL Server Central | |
| Linux SQL Databases and Tools | |
| Biology Portals (6) | |
| ENTREZ | The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website |
| National Center for Biotechnology Information (NCBI) | |
| Open Wetware | Useful protocols section to find out what how things are done |
| The Arabidopsis Information Resource (TAIR) | |
| Biotech Industry Supplier Registry | Manual compilation of biotech suppliers enabling buyers to easily source manufacturers of biotechnology equipment for cell biology, cell culture, genomics, proteomics and more. Site includes new projects, free magazines, jobs, news and events. |
| moutou | Inoveol actives are natural polyphenols which have been converted by a green biotechnology process into perfectly stable (high resistance to spontaneous oxidation) and water soluble (direct incorporation into any formula) active ingredients. Safe, natural and innovative, Inoveol actives combine the most powerful beneficial properties of plants for skin care and the most recent research advances in biotechnology. |
| Bioinformatic Portals (8) | |
| Bioinformatics.Org | |
| BioPerl | libraries for perl that have useful biological functions |
| EMBOSS | EMBOSS is "The European Molecular Biology Open Software Suite" which includes a variety of different applications for sequence analysis. http://emboss.sourceforge.net/ |
| Biopython | similar to bioperl but for python |
| Sequence Manipulation Tools | Useful suite of tools to do many common sequence manipulation tasks |
| UCSC genome browser | View Abstracts |
| Generic Model Organism Database | Collection of open source software tools for creating and managing genome-scale biological databases |
| Biotech Industry Supplier Registry | Manual compilation of biotech suppliers enabling buyers to easily source manufacturers of biotechnology equipment for cell biology, cell culture, genomics, proteomics and more. Site includes new projects, free magazines, jobs, news and events. |
| Statistics (5) | |
| The R Project | |
| TASSEL | TASSEL evaluates linkage disequilibrium, nucleotide diversity, and trait associations |
| Bioconductor | Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data
|
| SAPS | SAPS (Statistical Analysis of Protein Sequences) evaluates by statistical criteria a wide variety of protein sequence properties. |
| RPy | Interface for using R in python |
| Web Applications (9) | |
| BLAST | The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences |
| FGENE web interface | Gene prediction program web interface see link to program below |
| PLACE | View Abstracts
Database of plant cis-acting regulatory DNA elements (final update 1/2007) |
| European Union DGXII Biotechnology FW IV Research Programme | Development, optimization and validation of molecular tools for assessment of biodiversity in forest trees |
| mVista | mVISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. Web interface for LAGAN, AVID |
| SIM4 web interface | A program to align cDNA and genomic DNA, see sim4 entry below |
| CD Search | search the Conserved Domain Database with Reverse Position Specific BLAST. |
| ENZYME | ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided . |
| Fast sequence alignment | View Abstracts
FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo. |
| Alignment and Phylogenetics Software (9) | |
| BLAST | The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences |
| zPicture | Z-Picture is a dynamic alignment and visualization tool used for comparative genomics |
| Clustal | View Abstracts
ClustalW is a general purpose multiple alignment program for DNA or proteins |
| CompareProspector | View Abstracts
CompareProspector uses comparative genomics information to aid in sequence motif finding.
|
| PhyloVista | PHYLO-VISTA is an interactive tool for analyzing multiple DNA sequence alignments by vizualizing a similarity measure for DNA sequences for different species while considering their phylogenic relationships |
| TaxPlot | a tool for 3-way comparisons of genomes on the basis of the protein sequences they encode. |
| Dotter | A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis |
| Jdotter | Java interactive interface for the Linux version of Dotter |
| Gepard | Dotplots for large data sets |
| Gene Prediction (13) | |
| GeneMark | View Abstracts
Determines the protein-coding potential of a DNA sequence by using species specific parameters of the Markov models of coding and non-coding regions. |
| GENSCAN | View Abstracts
Genscan predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms |
| FGENESH | View Abstracts
FGENESH uses HMMs and protein similarity to perform gene prediction |
| GRAILEXP | View Abstracts
Grail-EXP is a software package that predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence |
| GeneMachine | View Abstracts
GeneMachine is an integrated tool intended to perform both comparative and predictive gene identification (requires registration) |
| HMMgene | View Abstracts
HMMgene is a program for prediction of genes in anonymous DNA |
| Geneid | View Abstracts
Geneid is a program that predict genes, exons, splice sites and other signals along a DNA sequence |
| Glimmer | View Abstracts
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses |
| MZEF | View Abstracts
MZEF provides a new method for predicting internal coding exons in genomic DNA sequences. This computer program allows users to predict putative internal protein coding exons, adjust prior probability and to output alternative overlapping exons. It is based on a prediction algorithm using the quadratic discriminant function for multivariate statistical pattern recognition |
| EST2Genome | Est2genome is a software tool to aid the prediction of genes by sequence homology |
| Spidey | Spidey is an mRNA-to-genomic alignment program |
| RBSfinder | RBSfinder will search for regions in the vicinity of the gene start where the ribosome might bind. Based on its findings RBSfinder might propose a different gene start. |
| GeneZilla | View Abstracts
GeneZilla is a state-of-the-art program for computational prediction of protein-coding genes in eukaryotic DNA, and is based on the Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN and GENIE. (formerly TIGRscan) |
| Mapping and Assembly (16) | |
| Phred | View Abstracts
Primary tool used in base calling and quality value determination for sequencing data. |
| Phrap | Primary tool used in shotgun DNA Sequence assembly |
| Consed | View Abstracts
This tool generates a visual/graphical overview of assembled sequence data, allowing for the manual detecting and fixing of assemblies. |
| Staden Package | View Abstracts
Assembler package that includes programs such as PreGap4 and Gap4. |
| Genetic Mapping Primer/Tutorial | |
| Genetic Mapping Primer from NCBI | |
| T-DNA Express | View Abstracts
Gene Mapping Tool for Arabidopsis |
| Qtl Cartographer | A suite of programs to map quantitative traits using a map of molecular markers |
| Mapmaker 3 | View Abstracts
Contains two programs:
1. Mapmaker/Exp - A linkage analysis package designed to help construct primary
linkage maps of markers segregating in experimental crosses.
2.MAPMAKER/QTL - a companion program to MAPMAKER/EXP which allows one to map
genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map |
| Qtl Express | View Abstracts
Provides an analysis of quantitative trait data from outbred populations (last update Feb 2008, replaced with GridQTL that requires registration) |
| QTX | View Abstracts
QTX detects and localizes quantitative trait loci (development ended) |
| MapQTL | MapQTL is computer software for the calculation of positions of quantitative trait loci (QTLs) on genetic maps |
| MultiQTL | MultiQTL software integrates a broad spectrum of data mining, statistical analysis, interactive visualization and modeling tools that allow QTL analysis based on advanced and sophisticated methods for maximum extraction of the mapping information from data |
| Map Viewer | The Map Viewer provides a wide variety of genome mapping and sequencing data. |
| EagleView | View Abstracts
EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. |
| Gblocks | View Abstracts
Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. |
| Sequence Annotation (25) | |
| ESTScan | View Abstracts
ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts |
| ORF Finder | The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a users sequence or in a sequence already in the database |
| AlignAce | View Abstracts
AlignACE (Aligns Nucleic Acid Conserved Elements) is a program which finds sequence elements conserved in a set of DNA sequences |
| BEARR | View Abstracts
BEARR (Batch Extraction and Analysis of cis-Regulatory Regions) is a software suite for analyzing transcriptional regulatory regions in the genome |
| BioProspector | View Abstracts
BioProspector, a C program using a Gibbs sampling strategy, examines the upstream region of genes in the same gene expression pattern group and looks for regulatory sequence motifs |
| CONFAC | View Abstracts
Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites |
| Eponine | View Abstracts
Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence |
| FirstEF | View Abstracts
FirstEF is a 5 terminal exon and promoter prediction program |
| IslandPath | View Abstracts
IslandPath incorporates both DNA sequence signal features and annotation features to aid the identification of genome islands. Mostly for prokaryotes |
| IsoFinder | View Abstracts
The IsoFinder web server allows accurate and reliable isochore predictions in genome sequences (GC content) |
| JASPAR | View Abstracts
JASPAR is a collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. |
| McPromoter | View Abstracts
McPromoter is a program aiming at the exact localization of eukaryotic RNA polymerase II transcription start sites. mostly focused on D. melanogaster DNA |
| PromoSer | View Abstracts
PromoSer is a web-based service aimed specifically at the extraction of a large number of promoter sequences from mammalian genomes. To identify the transcription start site (TSS) of a gene, we map all available mRNA and EST sequence data onto the genome and track the overlapping alignments (denoted as a cluster) |
| rVista | View Abstracts
rVista combines database searches with comparative sequence analysis to find potential regulatory elements in noncoding regions of the human genome |
| seqVista | View Abstracts
eqVISTA presents a holistic, graphical view of features annotated on nucleotide or protein sequences. Allows easy searching for sequence motifs or extraction of particular subsequences |
| tRNAscan-SE | View Abstracts
Search for tRNA genes in genomic sequence |
| VecScreen | A tool for identifying segments of a nucleic acid sequence that may be of vector, linker, or adapter origin prior to sequence analysis or submission. |
| Gibbs Motif Sampler | View Abstracts
Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS). |
| SNAP | View Abstracts
SNAP (SNP Annotation and Proxy Search) finds proxy SNPs based on linkage disequilibrium, physical distance and/or membership in selected commercial genotyping arrays. |
| Signal Search Analysis | View Abstracts
SSA is a software package for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site such as a transcription initiation site. |
| T-coffee, M-Coffee, expresso | View Abstracts
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures. |
| MaxAlign | View Abstracts
A tool to remove sequences (taxa) with many gaps in the post-process of alignments in order to improve the alignment area. Maximizes the number of characters that are present in gap-free columns (alignment area) by selecting an optimal subset of sequences |
| sim4 | View Abstracts
Sim4 is similarity-based tool designed to align an expressed DNA sequence with a genomic sequence, allowing for introns. SIBsim4 is a derivative work from sim4
|
| MAKER | View Abstracts
Genome annotation pipeline for eukaryotic genomes and creates genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and automatically synthesizes these data into gene annotations having evidence-based quality indices. |
| Apollo Genome Annotation Curation Tool | View Abstracts |
| Proteins and Pathways (20) | |
| DALI | View Abstracts
Dali is a network service for comparing protein structures in 3D |
| STRUCTAL | View Abstracts
STRUCTAL provides database comparison of 3D protein structure (no clue how old this is, hard to find info about it from main page) |
| UNIPROT | UNIPROT is a comprehensive database resource for protein sequence and annotation data, comprised of: UniProtKB, UniRef, UniParc |
| PROSITE | PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them |
| CN3D | Cn3D is a 3-dimensional visualization tool for biomolecular structures, sequences, and sequence alignments |
| CATH | View Abstracts
CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis. |
| SSAP | The SSAP server allows users to compare the structures of two proteins and view the subsequent structural alignment |
| VAST | VAST Search is the NCBI structure-structure similarity search service |
| SSM | View Abstracts
Secondary Structure Matching (SSM) is an interactive service for comparing protein structures in 3D |
| SCOP | View Abstracts
SCOP is a database, created by manual inspection and abetted by a battery of automated methods, that aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known (Alexey Murzin) |
| KEGG | KEGG is a database of biological systems, consisting of genetic building blocks of genes and proteins, chemical building blocks of both endogenous and exogenous substances, molecular wiring diagrams of interaction and reaction networks, and hierarchies and relationships of various biological objects. |
| PICR | View Abstracts
Protein Identifier Cross-Reference Service is a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. |
| PDB | The PDB(Protein Data Bank) archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. |
| Pfam | The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). |
| PSIPRED | View Abstracts
The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice and receive the results of the prediction via e-mail. |
| TMHMM | View Abstracts
Prediction of transmembrane helices in proteins based on hidden Markov model. Main website has very nice tools and services |
| SignalP | SignalP 3.0 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. |
| ALDENTE | View Abstracts
Aldente is a tool to identify proteins from peptide mass fingerprinting data. This new, fast and powerful tool takes advantage of the Hough transform for spectra recalibration and outlier exclusion. |
| Motif Scan | Motif scanning means finding all known motifs that occur in a sequence. This form lets you paste a protein sequence, select the collections of motifs to scan for, and launch the search. |
| Biotech Industry Supplier Registry | Manual compilation of biotech suppliers enabling buyers to easily source manufacturers of biotechnology equipment for cell biology, cell culture, genomics, proteomics and more. Site includes new projects, free magazines, jobs, news and events. |
| Sequence Retrieval and Submissions (9) | |
| ENTREZ | The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website |
| Sequin | Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases |
| BankIt | BankIt is a web-based sequence submission tool
|
| FASTA | FASTA provides sequence similarity searching against nucleotide and protein databases using the FASTA programs |
| dbSNP | Database of known Single Nucleotide Polymorphisms |
| GenBank | GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences |
| MatchMiner | MatchMiner is a set of tools that enables the user to translate between disparate ids for the same gene. It uses data from the UCSC, LocusLink, Unigene, OMIM, Affymetrix and Jackson data sources to determine how different ids relate. Supported id types include, gene symbols and names, IMAGE and FISH clones, GenBank accession numbers and UniGene cluster ids. |
| Miamexpress | MIAME (minimum information about a microarray experiment) compliant microarray data submission tool |
| IBM Genome Annotation | IBM Bio-Dictionary-based Annotations Of Completed Genomes page lists annotations for over 75 complete genomes (very old) a complete list can be found here: http://cbcsrv.watson.ibm.com/Annotations/ and some tools here: http://cbcsrv.watson.ibm.com/Tspd.html |
| Expression (microarray) (17) | |
| Laboratory for Genomics and Bioinformatics - University of Georgia | MAGIC Database, The database can be thought of as consisting of two major components - a segment that focuses on gene discovery through DNA sequencing, with a focus on EST projects, and a second that deals with microarray data. |
| Genevestigator | View Abstracts
reference expression database and meta-analysis system |
| caGEDA | View Abstracts
A web application for the integrated analysis of global gene expression patterns in cancer |
| UNIGENE | An Organized View of the Transcriptome |
| Expression Profiler | View Abstracts
An open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics (thru R), machine-learning algorithms and visualization |
| ACID | View Abstracts
ACID is a web-based comprehensive database server for information about reporters/probes/genes used in microarray experiments. |
| ArrayXPath | View Abstracts
ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. |
| BAGEL | View Abstracts
Bayesian Analysis of Gene Expression Levels is a program that allows
statistical inferences to be made regarding differential gene expression between two or
more samples measured on spotted microarrays |
| CIBEX | The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data |
| CARRIE | View Abstracts
CARRIE is a program takes two condition microarray data and applies promoter analysis to infer the stimulated/repressed transcriptional regulatory network. |
| GOAL | View Abstracts
GOAL is a resource designed for functional analysis of DNA microarrays and maintained at the "Data Mining for Analysis of DNA Microarrays" |
| KARMA | View Abstracts
KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays |
| Microarray and Gene Expression Database | MGED aims to facilitate the sharing of data generated using the microarray and other functional genomics technologies for a variety of applications including expression profiling |
| Stanford Microarray Database | SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization |
| PrimerBank | View Abstracts
PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR) |
| RTPrimerDB | View Abstracts
RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories |
| GEO | The Gene Expression Omnibus (GEO) provides several tools to assist with the visualization and exploration of GEO data. |
| Repeat Masking (9) | |
| Tallymer | View Abstracts
kmer counting method for identifying repeats |
| RepeatMasker | Program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence |
| Tandem Repeat Occurrence Locator (troll) | View Abstracts
Lightweight SSR finder based on a slight modification of the Aho-Corasick algorithm. |
| Tandem Repeat Finder (TRF) | View Abstracts |
| RAP | View Abstracts
This tool allow to identify repeated sequences using word counting based algorithm. |
| Piler | View Abstracts
Can search for different types of repeats, bad for short sequences (<50bp) |
| RECON | View Abstracts
De novo identification and classification of repeat sequence families from genomic sequences. Our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes. |
| RepeatScout | View Abstracts
De Novo identify repeat family sequences from genomes where hand-curated repeat databases (a la RepBase update) are not available. |
| AAARF | View Abstracts
Using a combination of sample sequencing, bioinformatics and novel software design approaches to characterize the high copy number repeats. The program is composed of a single Perl program that utilizes the freely available bioperl module libraries. AAARF allows a high level of automation |
| Plant Model Organisms (36) | Included in this category are links to resources for various plant model organisms. These include databases and tools for genome scale analyses. |
| Journals (28) | |
| Theoretical and Applied Genetics (TAG) | |
| Genetics | |
| Tree Genetics and Genomes | |
| Trends in Plant Science | |
| Molecular Breeding | |
| Silvae Genetica | |
| New Phytologist | |
| Public Library of Science (PLoS Biology) | |
| Plant Systematics and Evolution | |
| Plant Cell Reports | |
| Unasylva | |
| Tree Physiology | |
| New Forests | |
| Trees- Structure and Function | |
| Plant Molecular Biology Reporter | |
| Plant Molecular Biology | |
| Molecular Breeding | |
| Conservation Genetics | |
| Journal of Structural and Functional Genomics | |
| Current Genetics | |
| Planta | |
| Plant Journal | |
| Annual Review of Plant Biology | |
| Genomics | |
| Trends in Genetics | |
| International Journal of Plant Sciences | |
| Genome Research | |
| Journal of Plant Growth Regulation | |
| Resources (7) | |
| Agricola | |
| BIOSIS | |
| Pubmed | |
| Douglas-fir Genome Project | |
| Commonwealth Agricultural Bureaux (CAB) abstracts | |
| Virtual Library on Genetics | |
| E-Journals | Electronic sites of botany, plant biology, and science journals |
| Search Tools (1) | |
| Online Journals Search Engine | |
| Research Groups (95) | This category contains links to groups and organizations contributing to conifer genetics and tree improvement research. |
| General Resources (15) | |
| Canada's Forest Network | The Canadian Wood Council CWC is the national association representing Canadian manufacturers of wood products used in construction. CWC works with building codes and standards and by developing and communicating technical information to architects, engineers and builders |
| PlantGDB | View Abstracts
Resources for Plant Comparative Genomics such as sequence download, annotation, and comparison tools |
| TreeBase | View Abstracts
A relational database designed to manage and explore information on phylogenetic relationships |
| USDA Plants Species Database | The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories. |
| Gymnosperm Database | Basic information about gymnosperms for the public. Taxonomic tree |
| Native Conifers of North America | Pretty pictures of trees and how to identify |
| American Conifer Society Database | Community dedicated to conifers with web links, photos and forums. |
| Plants for a Future Database (Pinaceae) | Database of plants with information about habitat and uses (website sometimes goes down at end of month) |
| BoDD - Botanical Dermatology Database | Summary of plants in Pine family and where they are found |
| ITIS - Integrated Taxonomic Information System | Government website with authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. |
| MIPSPlantsDB - MIPS Plants Databases | View Abstracts
The MIPS plant genomics group focuses on the bioinformatics of plant genomes. |
| Plant Transcription Factor Database | View Abstracts
PlnTFDB is a public database arising from efforts to identify and catalogue all Plant genes involved in transcriptional control. |
| ChromDB | View Abstracts
Displays chromatin-associated proteins, including RNAi-associated proteins, for a broad range of organisms. Our primary focus is to display sets of highly curated plant genes predicted to encode proteins associated with chromatin remodeling. |
| TIGR Plant Genomics Group | TIGR's Genome Projects are a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans. |
| Plant MPSS Databases | View Abstracts
Good starting point when working with plants with sequence downloads |
| Fruits (1) | |
| GDR (Genome Database for Rosaceae) | View Abstracts |
| Arapidopsis (22) | |
| GABI (Genome Analysis of the Plant Biological System) | |
| Gramene | View Abstracts
A resource for comparative grass genomics |
| The Arabidopsis Information Resource | View Abstracts
a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana |
| The TIGR Arabidopsis thaliana Database | Provides a collection of information on genome research, including chromosomes, RNA gene table, gene survey charts, and sequence data. |
| The MIPS Arabidopsis thaliana genome database | View Abstracts |
| ATIDB : The Arabidopsis thaliana Integrated Database | Database Integrates Arabidopsis Genome, Gene Ontology db, Transposon and T-DNA flanking sequence, and more |
| AtGDB: An Arabidopsis thaliana Plant Genome Database | |
| Database of Arabidopsis Transcription Factors - DATF | View Abstracts
not-updated |
| Arabidopsis MPSS Plus Database Test | |
| The Arabidopsis Lipid Gene Database | not-updated |
| Arabidopsis Small RNA Project - ASRP | View Abstracts |
| Arabidopsis Transcriptome Genomic Express Database | |
| Complete Arabidopsis Transcriptome Microarray - CATMA | View Abstracts |
| Arabidopsis Unannotated Secreted Peptide Database | View Abstracts |
| The Goldberg Lab Arabidopsis thaliana GeneChip Database | |
| The Arabidopsis Gene Regulatory Information Server - AGRIS | View Abstracts |
| Arabidopsis Splicing Related Genes (ASRG) | View Abstracts |
| RARGE - RIKEN Arabidopsis Genome Encyclopedia | View Abstracts
RIKEN is japanese institute institute
RARGE is their genome encyclopedia |
| Arabidopsis Mutations Library Database | |
| AFGN - Arabidopsis Functional Genomics Network | |
| Arabidopsis thaliana Transcription factors | View Abstracts |
| Arabidopsis thaliana Chromatin Database | View Abstracts |
| Trees (12) | |
| Arborea | This genomic project will identify and characterize the function of genes that control major properties of economic importance in forest trees, namely genes that control wood formation and forest health. Has poplar and spruce ESTs. |
| BIOGECO - UMR | |
| MycorWeb - INRA | Tree micro-organism interactions |
| IPGC - International Populus Genome Consortium | |
| PopulusDB | View Abstracts |
| Douglas-fir Genome Project | |
| Populus trichocarpa Transcription factors | |
| Populus trichocarpa genome - JGI | |
| Populus trichocarpa Chromatin Database | |
| AspenDB | |
| PoplarPLEX | MIAME/Plant-compliant and Plant Ontology enhanced expression database for poplar microarray data |
| Genome Sciences Centre | Physical Mapping Data Access |
| Conifer (8) | |
| Conifer Comparative Genomics Project - UCDavis | |
| Douglas-fir Genome Project - UCDavis | |
| BIOGECO - UMR | |
| Laboratory for Genomics and Bioinformatics - University of Georgia | MAGIC Database, The database can be thought of as consisting of two major components - a segment that focuses on gene discovery through DNA sequencing, with a focus on EST projects, and a second that deals with microarray data. |
| Genomics of Wood Formation in Loblolly Pine - CCGB | link dead as of 7/2009 |
| Loblolly and Slash Pine Rooted Cutting Program - North Carolina State University | |
| Accelerating Pine Genomics - MGEL - Mississippi State University | |
| Genomics of Loblolly Pine Embryogenesis Project - IPST and TIGR | |
| Grains (36) | |
| GABI (Genome Analysis of the Plant Biological System) | |
| GrainGenes | View Abstracts
GrainGenes is a suite of services for the Triticeae and Oat communities, including databases, documents, tools, data files, web sites, announcements, curation, and community assistance. |
| Gramene | View Abstracts
A resource for comparative grass genomics |
| BarleyDB | |
| The maize genome database (MGSP) | |
| MaizeGDB | View Abstracts
MaizeGDB is the community database for biological information about the crop plant Zea mays ssp. mays. |
| MaizeSequence | |
| Functional Genomics of Maize Chromatin Consortium | |
| PGIR - Plant Genome Initiative at Rutgers | |
| HMPR and MSLL for maize | |
| Maize Full Length cDNA Project | |
| Maize Mapping Project | |
| Maize Sequencing | |
| Consortium for Maize Genomics | |
| Maize Gene Discovery | |
| Molecular and Functional Diversity of the Maize Genome | |
| Maize Genetic Mapping Project | |
| Maize Genetics Cooperation Stock Center | |
| Maize Oligonucleotide Array Project | |
| The TIGR Maize Database | View Abstracts |
| The MIPS Oryza sativa database (MOsDB) | View Abstracts |
| Oryza sativa subsp. japonica Transcription factors | |
| Oryza sativa spp. JaponicaChromatin Database | |
| MGOS - Magnaporthe Grisea Oryza Sativa Interaction Database | View Abstracts |
| Oryza Map Alignment Project (OMAP) | |
| Sequencing Information (ACWW/IRGSP) | |
| Rice Genome Sequencing | |
| NSF Rice Oligonucleotide Array Project | |
| Oryzabase | View Abstracts |
| Rice Database | The Rice Annotation Project (RAP), Integrated Rice Genome Explorer (INE), Rice GAAS Rice Genome Automated Annotation System, Rice Annotation Database (RAD), Rice Proteome Database, Knowledge-Oriented Molecular Biological Encyclopedia KOME, Rice Tos17 Insertion Mutant Database, Rice Expresstion Database RED, RGP Rice cDNA Sequence Database, RMOS Rice Microarray Opening Site, Rice PIPELINE, PLACE (PLAnt Cis-acting Regulatory DNA Elements Database), Rice Mitochondrial Genome Information RMG, RPSD Rice Protein Structure Database |
| TIGR Rice Genome Annotation Database and Resource | View Abstracts |
| Rice Kinase Database | |
| Rice MPSS | |
| RiceGE: Rice Functional Genomic Express Database | |
| The Korea Rice Genome Database | |
| International Rice Genome Sequencing Project (IRGSP) | View Abstracts |
| Grasses (2) | |
| FoggDB | FoggDB for the storage of genetic mapping data pertaining to the temperate forage grasses, Lolium Perenne, Lolium multiflorum and Festuca Pratensis |
| Gramene | View Abstracts
A resource for comparative grass genomics |
| Legume (3) | |
| The Medicago truncatula genome database | |
| TIGR Medicago truncatula Genome Project | |
| UMN Medicago resources | View Abstracts |
| Literature (118) | Relevant articles, journals, and other resouces providing background and supporting information for the field. |
| Australia and New Zealand (11) | |
| CSIRO - Molecular Breeding of Forest Trees | The main focus of research conducted by the Molecular Breeding Group at CSIRO Forestry and Forest Products is using molecular technologies to more efficiently develop improved breeds of commercial tree species. |
| CPCG - Centre for Plant Conservation Genetics | |
| Cooperative Research Centre for Sustainable Production Forestry | |
| STBA - Southern Tree Breeding Association - Australia | |
| Plant Science (Eucalyptus Genetics) - University of Tasmania | |
| Forest Molecular Biology and Genetics Group - University of | |
| International Eucalyptus Genome Network EUCAGEN | |
| SCION | |
| Dominic Cain - Australian National University | |
| Colin Matherson - Australian National University | |
| BioSylve Forest Science NZ Limited | |
| European Union (31) | |
| Austrian Federal Forest Research Center | |
| Department of Forest Genetics and Plant Physiology - Sweden | |
| GABI (Genome Analysis of the Plant Biological System) | |
| BIOGECO - UMR | |
| MycorWeb - INRA | Tree micro-organism interactions |
| Plant Molecular Biology and Biotechnology - CSIC | |
| UK Crop Net | |
| Wood Biotechnology - KTH | |
| Department of Forest Genetics and Forest Tree Breeding - University of Göttingen | |
| Swedish University of Agricultural Sciences (Von Arnold) | |
| Forest Genetics in Umeå Plant Science Centre - Umeå University | |
| Department of Dendrology and Forest Tree Breeding - University of Agriculture Czech Republic | |
| Oak Tree Research - University of Bodenkultur Wien | |
| The Plant Genetics Group - University of Oulu | |
| Gail Taylor Plant and Environment Lab | |
| Vantaa Research Unit - Finnish Forest Research Institute | |
| Polytechnic of Castelo Branco | |
| Forest Genetic Resources - FAO Forestry of the UN | |
| International Plant Genetic Resources Institute - Bioversity International - Forest Genetic Diversit | |
| Physiology and Genetics - IUFRO Division 2 | |
| Tree Improvement and Forest Genetics - Forest Research - Northern Research Station | |
| Lithuanian Forest Research Institute | |
| Institute of Forest Genetics and Forest Tree Breeding, Germany | |
| Institute of Dendrology, Polish Academy of Sciences | Laboratory of Population Genetics and Laboratory of Biochemical Genetics
|
| Insitute of Plant Genetics and Biotechnology - Slovakia Academy of Science | |
| Forest Biotech Lab -Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa | |
| INRA - TREEBREEDEX | |
| INRA, Equipe de Gntique et Amlioration des Arbes Forestiers | |
| INRA Orleans - Forest Genetic Resources Conservation Laboratory (CCAF) | |
| BFW Forest Tree Breeding and Genetics | |
| Austrian Research Center | OAKFLOW and PICME (Platform for Integrated Clone Management) |
| Middle East and Asia (16) | |
| Forestry and Forest Products Research Institute - Japan | |
| TFRI - Tropical Forest Research Institute - India | |
| University of Forestry | |
| Dr. Yashwant Singh Parmar University of Horticulture and Forestry | |
| FABI - Forest and Agricultural Biotechnology Institute - University of Pretoria | |
| Advanced Biotechnology and Breeding Centre (ABBC) - Malaysian Palm Oil Board | |
| National Forest Tree Breeding Center - Japan | |
| Middle East Technical University | |
| Kyushu University | |
| Laboratory of Molecular Population Genetics LMPG - Kyushu University | |
| Korea Forest Research Institute | |
| Kerala Forest Research Institute | |
| Institute of Forest Genetics & Tree Breeding Coimbatore - ICFRE, Dehradun | |
| Forestry Research Institute of Malaysia | |
| Sugi Genome Database | |
| Forest Genetics and Breeding Division - Arid Forest Research Institute | |
| North America (60) | |
| Forest Genomics at Purdue University | |
| Arborea | This genomic project will identify and characterize the function of genes that control major properties of economic importance in forest trees, namely genes that control wood formation and forest health. Has poplar and spruce ESTs. |
| Canada's Forest Network | The Canadian Wood Council CWC is the national association representing Canadian manufacturers of wood products used in construction. CWC works with building codes and standards and by developing and communicating technical information to architects, engineers and builders |
| Conifer Comparative Genomics Project - UCDavis | |
| Douglas-fir Genome Project - UCDavis | |
| Forest Tree Biotechnology - North Carolina State University | |
| Genome Canada | |
| Institute of Forest Genetics in Placerville | |
| Institute for Plant Genomics and Biotechnology - Texas A&M | |
| Laurentian Forestry Center - Canadian Forest Service | |
| Laboratory for Genomics and Bioinformatics - University of Georgia | MAGIC Database, The database can be thought of as consisting of two major components - a segment that focuses on gene discovery through DNA sequencing, with a focus on EST projects, and a second that deals with microarray data. |
| Genomics of Wood Formation in Loblolly Pine - CCGB | link dead as of 7/2009 |
| Loblolly and Slash Pine Rooted Cutting Program - North Carolina State University | |
| Accelerating Pine Genomics - MGEL - Mississippi State University | |
| National Forest Genetics Laboratory | |
| Genomics of Loblolly Pine Embryogenesis Project - IPST and TIGR | |
| PlantGDB | View Abstracts
Resources for Plant Comparative Genomics such as sequence download, annotation, and comparison tools |
| Biotech Research Center - Michigan Tech | |
| Pine Genome Network | |
| Douglas-fir Genome Project | |
| Forest Genetic Resources Working Group | The Forest Genetic Resources Working Group (FGRWG)is a working group of the North American Forest Commission/FAO/UN. Its mission is to encourage and promote conservation of forest genetic resources by promoting the collection, exchange, and dissemination of information; by promoting cooperation and coordinating research, conservation, training, and exchange among member countries on genetic resource conservation problems; and by facilitating the international exchange of forest genetic resources. |
| Southern Institute of Forest Genetics | |
| The ESF Forest Biotechnology Working Group - SUNY College of Environmental Science and Forestry | |
| Texas Forest Service Forest Genetics | |
| Forest Genetics and Tree Improvement - Centre for Enhanced Forest Management - University of Alberta | |
| Centre for Forest Conservation Genetics - University of British Columbia | |
| Douglas Lab - Department of Botany, University of British Columbia | Fiber development and forestry genomics |
| Michael Smith Laboratories - University of British Columbia | |
| Forest Genomics Labs - University of Florida | |
| CFGRP - Cooperative Forest Genetics Research Program | Includes the University of Florida, IFAS, School of Forest Resources and Conservation, forest industrial and state agencies as cooperators to develop genetically-improved pine. |
| Warnell School of Forestry and Natural Resources - University of Georgia | |
| Forest Biotechnology of Warnell School of Forestry - University of Georgia | |
| Forest Resources - University of Idaho | |
| EPOBIO BioMatNet - Technology - Forestry | |
| Atree Conservation Genetics | |
| Forest Genetics Institute - University of Veracruzana | |
| Klein's Lab - University of New Hampshire | |
| Tree Biosafety and Genomics Research Cooperative - Oregon State University | |
| Center for Advanced Forestry - National Science Foundation | |
| The Schatz Center for Tree Molecular Genetics - Penn State University | |
| The Pacific Northwest Tree Improvement Research Cooperative PNWTIRC - Oregon State University | |
| Huang's Lab - Plant Biotechnology Network - Oklahoma State University | |
| Tauer's Lab - Department of Natural Resource Ecology and Management - Oklahoma State University | |
| Forest Genetics, Tree Physiology, AND Tree Improvement - Ohio State University | |
| Gerald A Tuskan Plant Genomics Group - Oak Ridge National Laboratory | |
| Lee E Gunter Plant Molecular Ecology Group - Oak Ridge National Laboratory | |
| FGO - Forest Genetics Ontario | |
| School Of Renewable Resources - Lousiana State University | |
| Forestry and Forest Environment Deparment - Lakehead University | |
| Biotechnology and Bioproduct - Natural Resources Canada | |
| Institute of Paper Science and Technology - Georgia Tech - USA | |
| Forest Genetics and Biotechnology - North Carolina State University | |
| Rhodes' Wildlife Ecology and Genetics Research Group - Purdue University | |
| Genomice Tool Development for The Fagacaceae | |
| Forest Conservation and Tree Genetics Program - University of Notredame | |
| Forest Genetics Section - British Columbia Forest and Range Research Branch | |
| Department of Biology - Appalachian State University | |
| Rick's Lab - University of Massachusetts Boston | |
| Dodd's lab - University of Berkeley | |
| Centre for Forest Conservation Genetics | The CFGC is the research group of Sally Aitken in the Department of Forest Sciences at the University of British Columbia investigating the conservation, ecological and population genetics of native tree species, as well as implications of climate change for these species, and making recommendations on conservation strategies to provincial and federal agencies. |
| South America (0) | |
| Laboratory Services (9) | Resources available for DNA Extraction and Genotyping services. |
| DNA Extraction (3) | |
| NFGEL | |
| Gene Service | |
| DNA Landmarks | |
| Genotyping Services (6) | |
| Affymetrix Gene Chip Genotyping Services | |
| Illumina SNP Genotyping Services | |
| Seq Wright | |
| Bio Trove | |
| UC Davis Genome Center | |
| Polymorphic DNA Technologies | |
| Conservation (11) | Informational sites relating to tree improvement and conservation. |
| Conservation (11) | |
| International Plant Genetic Resources Institute (IPGRI) | |
| Kew Gardens | Royal Botanical Gardens, Kew. |
| Center for Plant Conservation (US) | |
| Berry Botanic Garden | |
| EUFORGEN | European Forest Genetic Resources Programme |
| Missouri Botanical Gardens | |
| Forest Genetic Resources Working Group | The Forest Genetic Resources Working Group (FGRWG)is a working group of the North American Forest Commission/FAO/UN. Its mission is to encourage and promote conservation of forest genetic resources by promoting the collection, exchange, and dissemination of information; by promoting cooperation and coordinating research, conservation, training, and exchange among member countries on genetic resource conservation problems; and by facilitating the international exchange of forest genetic resources. |
| Centre for Forest Conservation Genetics | The CFGC is the research group of Sally Aitken in the Department of Forest Sciences at the University of British Columbia investigating the conservation, ecological and population genetics of native tree species, as well as implications of climate change for these species, and making recommendations on conservation strategies to provincial and federal agencies. |
| Scenic America - Tree Conservation | |
| United Nations Environment Programme - World Conservation Monitoring Centre | |
| Urban Forestry in Alabama | |
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