Stem Cell & Genome

ABOUT Fordebut NATIONAL CENTRE FOR NATURAL SCIENCE AND TECHNOLOGY
1. BIG PICTURE BOOK OF VIRUSEShttp://www.tulane.edu/%7Edmsander/Big_Virology/BVFamilyGenome.html
Electron micrographs of viruses.
2. HIV DATABASEShttp://hiv-web.lanl.gov/content/index
The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccines.
3. HIV DRUG RESISTANCE DATABASEhttp://hivdb.stanford.edu/
A curated database designed to analyze divergent forms of data underlying HIV drug resistance.
4. HIV MOLECULAR IMMUNOLOGYhttp://www.hiv.lanl.gov/content/immunology/index.html/
The HIV Molecular Immunology Database is an annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites.
5. ICTVdB PICTURE GALLERYhttp://www.ncbi.nlm.nih.gov/ICTVdb/Images/index.htm
Images of viruses.
6. INFLUENZA SEQUENCE DATABASE http://www.flu.lanl.gov/
All published influenza A, B, and C sequences, and search tools.
7. PLANT VIRUSES (CABRI CATALOG)http://www.cabri.org/HyperCat/plantvirus/DSMZ_plv.htm
Information about plant viruses.
8. PLANT VIRUSES ONLINEhttp://image.fs.uidaho.edu/vide/
Descriptions of plant viruses from the Virus Identification Data Exchange (VIDE) database.
9. RETROVIRUSES (NCBI)http://www.ncbi.nlm.nih.gov/retroviruses/
Retroviral research resources.
10. SUBVIRAL RNA DATABASEhttp://subviral.med.uottawa.ca/cgi-bin/accueil.cgi?typeRNA=1

1. ALFRED: ALLELE FREQUENCY DATABASEhttp://alfred.med.yale.edu/alfred/AboutALFRED.asp
ALFRED consists of allele frequency data on anthropologically defined human population samples links data on polymorphisms to molecular genetics and human genome databases.
2. BLAT SEARCH GENOMEhttp://genome.ucsc.edu/cgi-bin/hgBlat
BLAT Search Genome is designed to find sequences of 95% and greater similarity within the human genome (other genomes may be searched as well).
3. CABRI CELL LINES CATALOGShttp://www5.cabri.org/CABRI/home/description.html
CABRI (Common Access to Biological Resources and Information service) provides access to major European collections of cell lines and related resources.
4. CORIELL CELL REPOSITORIEShttp://locus.umdnj.edu/ccr/
The NIH-funded Coriell Cell Repositories establish, maintain, and distribute cell cultures and DNA derived from these cultures.
5. dbSNP HANDBOOKhttp://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=handbook.chap
Introduction to dbSNP.
6. dbSNP: SINGLE NUCLEOTIDE POLYMORPHISMhttp://www.ncbi.nlm.nih.gov/SNP/
dbSNP is a database of single nucleotide sequence alterations that occur in individuals. SNPs that are stable in populations and have value as diagnostic biomarkers. Entries are linked to GenBank, LocusLink, and PubMed information.
7. DIGIT: DIGIT INTEGRATES GENE IDENTIFICATION TOOLS (RIKEN)http://hgp.gsc.riken.go.jp/bioinformatics/digit.asp
DIGIT finds genes by combining existing genefinders, using hidden Markov models and Bayesian procedures.
8. ENCODE PROJECT PORTALhttp://genome.ucsc.edu/encode/
The goal of NHGRI's ENCODE project is to locate key functional elements that control gene expression, such as transcriptional regulatory sequence and the determinants of chromosome structure, in selected genomic regions.
9. GENE GATEWAYhttp://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/
Overview of the human genome project with links to bioinformatics tutorials.
10. GENEHUNTER http://www.fhcrc.org/labs/kruglyak/Downloads/index.html
A program for multipoint linkage analysis.
11. GeneLoc: GENE LOCATION (WEIZMANN INSTITUTE)http://genecards.weizmann.ac.il/geneloc//
GeneLoc provides an integrated map for each human chromosome, and includes links to GeneCards.
12. GENETHON DNA AND CELL BANKhttp://www.genethon.fr/php/layout_2.php?lang=us&navp=7&navt=ps&content=ps_banque&tools=0&subitem=ps_adn
The Genethon DNA and cell bank provides materials for genetics research.
13. GENOME NETWORK PROJECT (RIKEN)http://hgp.gsc.riken.go.jp/project/genomenetwork.asp
The goal of the Riken center Genome Netwowrk Project is to isolate and identify human transcription factor genes and promoter regions by both computational and experimental approaches.
14. HAPMAP LD SELECT PROCESSORhttp://sky.bsd.uchicago.edu/HapMap-LDSelect-Processor.html
Processes HapMap data using the LD Select method. Creates lists of SNPs within haplotype blocks.
15. HGVbase: HUMAN GENOME VARIATION DATABASEhttp://hgvbase.cgb.ki.se/
HGVbase is a curated catalog of normal human gene and genome variation, useful as a research tool to define the genetic component of human phenotypic variation.
16. HmutDB: HUMAN MUTATIONS DATABASEhttp://www.ebi.ac.uk/mutations/central/
HMutDB is a proposed database that will integrate data on gene mutations and natural polymorphisms.
17. HuGeMap DATABASEhttp://www.infobiogen.fr/services/Hugemap/
The HuGeMap database links genetic maps from Genethon and the Cooperative Linkage Center with physical maps from CEPH/Genethon and Whitehead.
18. HUMAN AGING GENOMIC RESOURCEShttp://genomics.senescence.info/
A collection of databases and tools for the study of the genetics of human ageing.
19. HUMAN CHROMOSOME LAUNCHPADhttp://www.ornl.gov/sci/techresources/Human_Genome/launchpad/
A single-source launchpad to information on each human chromosome.
20. HUMAN GENOME CENTRALhttp://www.ensembl.org/genome/central/
Human genome resources.
21. HUMAN GENOME PROJECT INFORMATIONhttp://www.ornl.gov/sci/techresources/Human_Genome/home.shtml
Information gateway for the Human Genome Project.
22. HUMAN GENOME PROJECT SEQUENCING SITEShttp://www.ornl.gov/sci/techresources/Human_Genome/research/centers.shtml
Links to members of the international genome sequencing consortium.
23. HUMAN GENOME RESEARCH GROUP (RIKEN)http://hgp.gsc.riken.go.jp/
One of the primary foci of the Riken center is the comparison of the human genome to chimp and mouse genomes.
24. HUMAN GENOME RESOURCEShttp://www.ncbi.nih.gov/genome/guide/human/
A guide to genomic information provided by NCBI.
25. HuSiDa: HUMAN siRNA DATABASEhttp://itb1.biologie.hu-berlin.de/~nebulus/sirna/
A repository for sequences of functional siRNA sequences.
26. INTERNATIONAL HAPMAP PROJECThttp://www.hapmap.org/
A multi-nation effort to identify genetic similarities and differences in human beings.
27. NIGMS HUMAN GENETIC CELL REPOSITORYhttp://locus.umdnj.edu/nigms/
The National Institute of General Medical Sciences provides materials for disease gene discovery, including cell cultures and DNA samples derived from these cultures.
28. OBESITY GENE MAP DATABASEhttp://obesitygene.pbrc.edu/
A database of markers, genes, and mutations linked to obesity phenotypes.
29. OMIM™: ONLINE MENDELIAN INHERITANCE IN MAN™http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
OMIM™ is a catalog of human genes and genetic disorders containing textual information and references. It also contains links to MEDLINE and sequence records.
30. PHINAL: PHASE INDEXED ALIGNMENT (RIKEN)http://hgp.gsc.riken.go.jp/bioinformatics/phinal.asp
PHINAL is global alignment tool for gene prediction that enables cross-species genome comparison by providing exact alignments around coding regions and a method for distinguishing coding regions from conserved non-coding regions.
31. POLYPHREDhttp://droog.gs.washington.edu/PolyPhred.html
Downloadable software that compares sequence traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.
32. REFSEQhttp://www.ncbi.nlm.nih.gov/RefSeq/
RefSeq sequences provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses.
33. RESOURCES (BROAD INSTITUTE)http://www.broad.mit.edu/resources.html
The Broad Institute resources page provides a variety of bioinformatics resources.
34. SeattleSNPs: VARIATION DISCOVERY RESOURCEhttp://pga.gs.washington.edu/
Applications for identifying SNPs in genes and pathways that underly inflammatory responses. Includes protocols.
35. SNP-ANALYSIShttp://www.fhcrc.org/labs/kruglyak/Downloads/index.html
A series of programs to analyze SNP data.
36. UCSC GENOME BIOINFORMATICShttp://genome.ucsc.edu/
The UCSC Genome Bioinformatics site provides the reference sequence and working draft assemblies for a collection of genomes, as well as tools for browsing.
37. VG: VISUAL GENOTYPEShttp://pga.gs.washington.edu/VG2.html
A graphic display format for individual genotype datasets that color-codes diallelic polymorphisms.
38. VH: VISUAL HAPLOTYPEShttp://pga.gs.washington.edu/VH1.html

1. BARLEY GENOME (NCBI)http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?chr=barley.inf
Genetic and physical maps for barley.
2. BARLEY SNPhttp://bioinf.scri.sari.ac.uk/cgi-bin/barleysnp/barley_SNPs
Single nucleotide polymorphism discovery and mapping in barley.
3. BARLEYBASEhttp://www.barleybase.org/
A repository for barley and Arabidopsis microarray data.
4. BIOINFORMATICS CENTERhttp://pgrc-14.ipk-gatersleben.de:7779/portal/page?_pageid=133,33954&_dad=portal&_schema=PORTAL
A portal to cultivated plant-related data warehouses and databases that can be combined with advanced experimental technologies to identify functional genetic elements and pathways that control gene expression.
5. CR-EST: CROP ESTshttp://pgrc.ipk-gatersleben.de/cr-est/index.php
Sequence, clustering and annotation data of crop gene expression projects.
6. DENDROME: FOREST TREE GENOME DATABASEhttp://dendrome.ucdavis.edu/
Forest tree genetics information resources.
7. DiStilling GENE FUNCTION IN BARLEYhttp://bioinf.scri.sari.ac.uk/distilling/distilling.html
A reverse genetics approach to barley gene function, based on the TILLING methodology (introduction of random point mutations followed by isolation and analysis of genomic DNA from leaf tissue).
8. GENEFARM: STRUCTURAL AND FUNCTIONAL ANNOTATION OF Arabidopsis thalianahttp://genoplante-info.infobiogen.fr/Genefarm/index.htpl
The goal of GeneFarm is to utilize a network of experts to generate reliable and traceable functional annotation of the A. thaliana genome.
9. GERMINATEhttp://bioinf.scri.sari.ac.uk/cgi-bin/germinate/germinate.cgi
A generic plant data management system, available for testing.
10. INE: INTEGRATED RICE GENOME EXPLORERhttp://rgp.dna.affrc.go.jp/giot/INE.html
Integrated genetic and physical mapping and sequencing information for the rice genome.
11. IPNI: THE INTERNATIONAL PLANT NAMES INDEXhttp://www.ipni.org/index.html
A database of names and bibliographic details for all seed plants.
12. MAIZEGDB: MAIZE GENETICS AND GENOMICS DATABASEhttp://www.maizegdb.org/
A repository for maize information including links to data centers and computational tools.
13. NASC: EUROPEAN ARABIDOPSIS STOCK CENTREhttp://nasc.nott.ac.uk/
Arabidopsis information resources.
14. NETPLANTGENE SERVERhttp://www.cbs.dtu.dk/services/NetPGene/index.php
Neural network predictions of splice sites in Arabidopsis thaliana DNA.
15. NewCROP™http://www.hort.purdue.edu/newcrop/
Information resources on crops. Includes CropINDEX, a list linking common and scientific names of crops.
16. openSPUTNK COMPARATIVE GENOMICS PLATFORMhttp://www.opensputnik.org/
A data pipeline and open-source infrastructure for plant genomics and comparative genomics.
17. PDW: PLANT DATA WAREHOUSEhttp://pdw.bic-gh.de/
Plant databases and algorithms useful for the identification of functional genetic elements in DNA sequences..
18. PLANT CENTRAL (NCBI)http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html
Links to information about plant genome projects in progress.
19. PLANT DNA C-VALUES DATABASEhttp://www.rbgkew.org.uk/cval/database1.html
A database useful for the evaluation of biodiversity based on the amount of DNA in the gametic nucleus (the C-value) as an estimate of genome size.
20. PLANT GENE REGISTERhttp://tarweed.com/pgr/
An repository for articles describing the identification and sequencing of plant genes.
21. PLANT GENOME RESOURCES CENTERhttp://pgrc.ipk-gatersleben.de/
A technological platform for plant genome analysis for barley and other crop species.
22. PLANT GENOMES QUERY (NCBI)http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?chr=plants.inf
Muli-plant genome search.
23. PLANT snoRNA DATABASEhttp://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
A database of information about Arabidopsis snoRNAs (the RNA component of small nucleolar RNA-protein complexes, or snoRNPs).
24. PLANTMARKERShttp://markers.btk.fi/
A database of predicted molecular markers for plants based on clustered plant transcriptomic data.
25. POMAMOhttps://gabi.rzpd.de/PoMaMo.html
Sequence and mapping information for the potato.
26. PROTLOCDB: PROTEIN LOCALISATION DATABASEhttp://bioinf.scri.sari.ac.uk/protlocdb.html
Color images of subcellular localization of numerous partial plant cDNA-GFP fusions.
27. RARGE: RIKEN ARIBIDOPSIS GENOME ENCYCLOPEDIAhttp://rarge.gsc.riken.jp/
Arabidopsis resource data, including cDNAs, transposon mutants, and microarray experiments.
28. REEF PLANT REFERENCE DATABASEhttp://www.infinitysoft.net/Reference/RefDB/list.asp?TYPE=PLANT
Information about plants associated with coral reefs.
29. RICE ANNOTATION DATABASEhttp://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html
A contig-oriented database for high-quality manual annotation of the rice genome.
30. RIKEN ARABIDOPSIS TRANSCRIPTION FACTOR DATABASEhttp://rarge.gsc.riken.go.jp/rartf/
A browsable list of nearly 2000 Arabidopsis transcription factors detected using PSI-BLAST searches, organized as transcription factor families.
31. SOYBASEhttp://129.186.26.94/
A collection of soy genetics and genomics information resources.
32. TAIR: THE ARABIDOPSIS INFORMATION RESOURCEhttp://arabidopsis.org/
An Arabidopsis information resource that includes search and analysis tools as well as links to stock centers.
33. TIGR Arabidopsis thaliana Databasehttp://www.tigr.org/tdb/e2k1/ath1/
Information on Arabidopsis genome research including ongoing projects to determine genome-wide transcription networks, and to predict novel genes using comparative genomics.

1. AMmtDhttp://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB
Multi-aligned sequences of vertebrate mitochondrial genes coding for proteins and tRNAs as well as D-loop (regulatory region) sequences.
2. Arabidopsis MITOCHONDRIAL PROTEIN DATABASEhttp://www.ampdb.bcs.uwa.edu.au/
The nuclear- and organielle-encoded mitochondrial proteins from Arabidopsis thaliana.
3. COMPLETE ORGANELLE GENOMEShttp://megasun.bch.umontreal.ca/ogmp/projects/other/mtcomp.html
A list of all published complete organelle sequences.
4. FMGP: FUNGAL MITOCHONDRIAL GENOME PROJECThttp://megasun.bch.umontreal.ca/People/lang/FMGP/FMGP.html
A project to sequence complete mitochondrial genomes from all major fungal lineages and to infer phylogeny.
5. GOBASEhttp://megasun.bch.umontreal.ca/gobase/gobase.html
Organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE will expand to include information on bacteria related to ancestors of mitochondria and chloroplasts.
6. MITOANALYZERhttp://www.cstl.nist.gov/biotech/strbase/mitoanalyzer.html
MitoAnalyzer compares SNPs and mutations in mitochondrial DNA with the Cambridge Reference Sequence in order to predict possible effects on protein sequences.
7. MITOCHONDRIOMEhttp://www.ba.itb.cnr.it/mitochondriome/
Mitochondriome integrates mitochondrial data and databases.
8. MITODAT: MENDELIAN INHERITANCE AND THE MITOCHONDRIONhttp://www-lecb.ncifcrf.gov/mitoDat/
MitoDat provides information about enzymes, structural proteins, and other proteins involved in mitochondrial biogenesis and function.
9. MITOMAP: HUMAN MITOCHONDRIAL DNA DATABASEhttp://www.mitomap.org/
Mitomap is a comprehensive database of human mitochondrial DNA variation and its relationship with human evolution and disease.
10. MITONUChttp://bighost.area.ba.cnr.it/srs6bin/wgetz?-page+LibInfo+-lib+MITONUC
A database for sequences of nuclear genes coding for mitochondrial proteins in metazoans and yeast.
11. MITOP: MITOCHONDRIAL PROTEOMEhttp://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html
A comprehensive list of mitochondrial proteins in yeast and humans lintegrated with signal sequence, proteome mapping, expression profiling, protein-protein interaction and localization data.
12. MITOPROThttp://ihg.gsf.de/ihg/mitoprot.html
MitoProt predicts mitochondrial targeting sequences.
13. MITOREShttp://www2.ba.itb.cnr.it/MitoNuc/
MitoRes is a database that integrates information about proteins that localize to metazoan mitochondria.
14. OGMP: ORGANELLE GENOME MEGASEQUENCING PROGRAMhttp://megasun.bch.umontreal.ca/ogmpproj.html
A collaboration focused on the molecular evolution of mitochondria.
15. ORGANELLE GENOMES RESOURCES (NCBI)http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html
A listing of organelle genomes that are part of the NCBI Reference Sequence (RefSeq) project.
16. ORGANELLEDBhttp://organelledb.lsi.umich.edu
Protein localization data for organisms spanning the eukaryotic kingdom, including a catalog of the constituents of 50 organelles, subcellular structures, and protein complexes. OrganelleDB includes images for localization of proteins in yeast.
17. PLMItRNAhttp://bighost.area.ba.cnr.it/PLMItRNA/
A database of tRNA genes in mitochondria of photosynthetic eukaryotes.
18. RNA EDITING WEB SITEhttp://dna.kdna.ucla.edu/rna/index.aspx

1. ANGLER: C. elegans DEVELOPMENT IN TIME AND SPACEhttp://www.sanger.ac.uk/Software/Angler/
Downloadable software for rapid browsing of cross-sectional Nomarsky images of C.elegans embryo development that allows differential coloring and highlighting of cells by lineage and by fate.
2. Caenorhabditis elegans WWW Serverhttp://elegans.swmed.edu/
A database of links to recent papers, meetings, software, protocols, and movies.
3. Caenorhabditis Genome Sequencing Projectshttp://www.sanger.ac.uk/Projects/C_elegans/
Links to information about Caenorhabditis sequence data.
4. CENTER FOR C.elegans ANATOMYhttp://www.aecom.yu.edu/wormem/
Protocols for transmission electron microscopy.
5. THE INTRONERATORhttp://www.cse.ucsc.edu/~kent/intronerator/
Tools for exploring the molecular biology and genomics of C.elegans with special emphasis on alternative splicing.
6. WORM LITERATURE INDEXhttp://elegans.swmed.edu/wli/
Searches abstracts from the literature.
7. WORMATLAShttp://www.wormatlas.org/index.htm
A database of behavioral and structural anatomy of Caenorhabditis elegans.
8. WORMBASEhttp://www.wormbase.org/

1. FANTOM: FUNCTIONAL ANNOTATION OF MOUSE (RIKEN)http://fantom.gsc.riken.jp/
Full-length cDNA clone information that includes functional annotation.
2. IMSR: INTERNATIONAL MOUSE STRAIN RESOURCEhttp://www.informatics.jax.org/imsr/index.jsp
An online database of mouse strains and stocks available worldwide.
3. MGI: MOUSE GENOME INFORMATICShttp://www.informatics.jax.org/
MGI provides integrated access to genetic, genomic, and biological datat for the mouse.
4. MOUSE GENOME BROWSER (ENSEMBL)http://www.ensembl.org/Mus_musculus/
Provides access to mouse gene sequences via a chromosome browser.
5. MOUSE GENOME RESOURCES (NCBI)http://www.ncbi.nlm.nih.gov/projects/genome/guide/mouse/
A gateway to mouse resources.
6. MOUSE NOMENCLATURE HOME PAGE (MGI)http://www.informatics.jax.org/mgihome//nomen/index.shtml
The official names for mouse genes, alleles, and strains.
7. MPD: MOUSE PHENOME DATABASEhttp://aretha.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/home
A collection of mouse phenotypic and genotypic data.
8. MOUSE TAXONOMY (NCBI)http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10088
A mouse taxonomy browser.
9. RAT GENOME BROWSER (ENSEMBL)http://www.ensembl.org/Rattus_norvegicus/
Ensembl assembles sequenced regions of the genome and analyzes the assembled DNA to find genes and other features.
10. RAT GENOME RESOURCES (NCBI)http://www.ncbi.nlm.nih.gov/genome/guide/rat/
A gateway to rat resources.
11. RATMAP: THE RAT GENOME DATABASEhttp://ratmap.gen.gu.se/
Information on rat gene nomenclature, chromosomal positions for genes, gene function, literature references and DNA sequences.
12. RGD: RAT GENOME DATABASEhttp://rgd.mcw.edu/
RGD curates and integrates rat genetic and genomic data.
13. THE RAT GENOME (NATURE WEB FOCUS)http://www.nature.com/nature/focus/ratgenome/
Links to papers on rat genomics.
14. UNIGENE SEQUENCES (RAT)http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=10116

1. 2-D PAGE DATABASEShttp://proteomics.cancer.dk/
This site links high-resolution 2D PAGE gels to proteomics databases.
2. 3DinSighthttp://gibk26.bse.kyutech.ac.jp/jouhou/jouhoubank.html
3DInSight searches biomolecular structure, property, and function (motifs, mutations, protein-nucleic acid binding, protein-ligand binding) and provides 3D structural and graphic output.
3. E-CELL PROJECThttp://e-cell.org/
The E-Cell Project aims to reconstruct cell systems in silico.
4. EMAP: EDINBURGH MOUSE ATLAS PROJECThttp://genex.hgu.mrc.ac.uk/
EMAP is a digital atlas of mouse development based on spatially mapped data such as in situ gene expression and cell lineage. EMAP data is integrated with EMAGE 2D and 3D expression data.
5. GENESNPs (ENVIRONMENTAL GENOME PROJECT)http://www.genome.utah.edu/genesnps/
GeneSNPs integrates gene, sequence, and polymorphism data into individually annotated gene models.
6. GPS TRAITMAPhttp://gps.gsc.riken.jp/gps/index.html
TraitMap, a component of the Genome-Phenome Superhighway, is a database of curator-checked mapping results based on published papers.
7. GPS TUTORIALhttp://gps.gsc.riken.jp/tutorial/tutorial_index.htm
How to access the Genome-Phenome Superhighway, including a description of the database architecture.
8. GPS: GENOME-PHENOME SUPERHIGHWAY (RIKEN)http://gps.gsc.riken.jp/gps/index.html
GPS integrates various databases based on the concept of omic space (i.e., phenome to genome), enabling the exploration of multiple biological interactions at various levels.
9. KEGG: KYOTO ENCYCLOPEDIA OF GENES AND GENOMEShttp://www.genome.jp/kegg/
KEGG has assembled a multitude of bioinformatics resources relating genomic information to higher-level processes.
10. MOUSE-HUMAN SYNTENY MAPhttp://gps.gsc.riken.jp/insilico/insilico_cloning_4.1.htm
Synteny information between mouse and human genes.
11. NRCAM: NATIONAL RESOURCE FOR CELL ANALYSIS AND MODELINGhttp://www.nrcam.uchc.edu/
NRCAM is developing a software modeling environment, the Virtual Cell, for quantitative cell biological research. Approaches in computational cell biology are coupled with high resolution light microscopy to facilitate the interplay between experimental manipulation and computational simulation of specific cellular functions.
12. OMIC SPACEhttp://gps.gsc.riken.jp/
Omic space is a comprehensive set of omic planes: phenome, metabolome, proteome, transcriptome, and genome used to build biological networks and generate predictions
13. PGRN: PHARMACOGENETICS RESEARCH NETWORK (NIH)http://www.nigms.nih.gov/pharmacogenetics/
The goal of PGRN is to study correlations between drug response phenotypes and genetic variation.
14. PHARMGKBhttp://www.pharmgkb.org/
The aim of PharmGKB is to understand how individual genetic variation contributes to differences in reactions to drugs. The database consists of genetic and clinical information derived from research studies at medical research centers.
15. PHARMGKB PATHWAYShttp://www.pharmgkb.org/search/pathway/pathway.jsp
Drug centered, gene-based, interactive pathways that highlight candidate genes and and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.
16. PHARMGKB TOOLShttp://www.pharmgkb.org/resources/sites/tools.jsp
Internet resources and software useful for pharmacogenomics research.
17. PROLINKShttp://128.97.39.94/cgi-bin/functionator/pronav
ProLinks predicts functional linkages between proteins from 168 species using phylogenetic profiles, gene clustering, the Rosetta Stone, and gene neighbor methods.
18. STANDARD ANATOMICAL NOMENCLATURE DATABASEhttp://genex.hgu.mrc.ac.uk/Databases/Anatomy/

1. ANAGE: ANIMAL AGEING DATABASEhttp://genomics.senescence.info/species/index.html
A curated database for the study of the comparative biology of aging.
2. ArkDBhttp://www.thearkdb.org/sites.html
Repository for genome mapping data for animals.
3. CGAP: CANCER GENOME ANATOMY PROJECThttp://www.ncbi.nlm.nih.gov/ncicgap/
Links to genetics tools and techniques.
4. COMPARATIVE MAPS (NCBI) http://www.ncbi.nlm.nih.gov/Homology/
Links to Homologene, TaxPlot, and COGs/KOGs comparative databases.
5. GENOME SURVEY SEQUENCEShttp://www.ncbi.nlm.nih.gov/dbGSS/
Single-pass genome survey sequences.
6. HAPMAP PROJECThttp://www.hapmap.org
Information about the HapMap Project. The goal of HapMap is to compare genetic sequences of individuals to identify regions where genetic variants are shared.
7. HTG: HIGH-THROUGHPUT GENOMIC SEQUENCEShttp://www.ncbi.nlm.nih.gov/HTGS/index.html
Unfinished genomic sequences generated by high-throughput sequencing centers.
8. MAGPIE: MULTIPURPOSE AUTOMATED GENOME PROJECT INVESTIGATION ENVIRONMENThttp://genomes.rockefeller.edu/research.shtml
MAGPIE accepts genomic sequence as input, adds annotation, and constructs models of molecular systems.
9. OMIA: ONLINE MENDELIAN INHERITANCE IN ANIMALShttp://www.angis.org.au/Databases/BIRX/omia/
A catalog of animal genes and disorders.
10. OMIM: ONLINE MENDELIAN INHERITANCE IN MANhttp://www3.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM&cmd=Limits
A searchable catalog of human genes and genetic disorders.
11. SNP CONSORTIUM http://snp.cshl.org/
News, linkage maps, and protocols.

1. ARGH: BIOMEDICAL ACRONYM RESOLVERhttp://invention.swmed.edu/argh/
A comprehensive catalog of biomedical acronyms and abbreviations.
2. GENEW: ADVANCED SEARCHhttp://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl
Advanced gene nomenclature search.
3. GENEW: HUGO GENE NOMENCLATUREhttp://www.gene.ucl.ac.uk/nomenclature/
The goal of the nomenclature group is to give a unique and meaningful name to each gene. The 20,000 names may be searched online or downloaded.
4. GiLL™: GI TO LOCUS LINK CONVERTERhttp://pathogene.swmed.edu/gill/
GiLL is a protein identification resolution database that resolves Locus Link IDs from GI numbers or RefSeq IDs. GILL provides official protein names, offical symbols, RefSeq accession numbers, Alliance for Cell Signaling IDs, Swiss-Prot IDs, and all gene ontology terms.
5. GUIDELINES FOR HUMAN GENE NOMENCLATUREhttp://www.gene.ucl.ac.uk/nomenclature/guidelines.html
The guidelines used by the Human Gene Nomenclature Committee.
6. IPNI: INTERNATIONAL PLANT NAMES INDEXhttp://www.ipni.org/index.html
A database of names of seed plants and related bibliographical information.
7. LOCUSLINK (NCBI)http://www.ncbi.nlm.nih.gov/LocusLink/
LocusLink provides information on official nomenclature, aliases, and accession numbers.
8. MOLECULE PAGES (AfCS)http://www.signaling-gateway.org/molecule/
The Alliance for Cell Signaling Molecule Pages include synonym information for over 3,000 proteins involved in cellular signaling.
9. REFSEQhttp://www.ncbi.nlm.nih.gov/RefSeq/index.html
RefSeq consists of a comprehensive, integrated, non-redundant set of sequences that serve as standards for functional studies.
10. W3 TROPICOShttp://mobot.mobot.org/W3T/Search/vast.html

1. ARRAYEXPRESS (EBI)http://www.ebi.ac.uk/arrayexpress/
Array Express is a public repository for microarray data.
2. BODYMAPhttp://bodymap.ims.u-tokyo.ac.jp/
BodyMap is a databank of expression information for human and mouse genes in various tissues or cell types at various times.
3. COMPARATIVE GENOMICS CENTER (LLNL)http://www.dcode.org/
Browsers for visualizing evolutionary conservation of multiple genomes, and for predicting gene regulatory sites using sequence conservation as a filter.
4. dbEST: EXPRESSED SEQUENCE TAGS DATABASEhttp://www.ncbi.nlm.nih.gov/dbEST/index.html
dbEST contains data on "single-pass" cDNA sequences (expressed sequence tags) from a number of organisms.
5. DoTS: DATABASE OF TRANSCRIBED SEQUENCEShttp://www.allgenes.org/
An index of all publicly available human and mouse transcript sequences.
6. DRAGON (DATABASE REFERENCING OF ARRAY GENES ONLINE)http://pevsnerlab.kennedykrieger.org/dragon.htm
Tools for the annotation and visualization of microarray data.
7. EGAD: EXPRESSED GENE ANATOMY DATABASEhttp://www.tigr.org/tdb/egad/egad.shtml
EGAD was constructed by extracting and curating GenBank sequences to create a set of non-redundant transcript sequences. In some cases, transcript sequences were assembled by splicing together distinct GenBank accessions for each exon, or by splicing exons from genomic sequence.
8. GeneX GENE EXPRESSION MARKUP LANGUAGEcompbio.ornl.gov/channel/
A description of GeneXML markup language, generated as a component of the GeneX project, a collaborative internet database for gene expression data.
9. GeneX-Lite: GENE EXPRESSION LITEhttp://www.ncgr.org/research/genex/
GeneX-Lite is a client application that allows the user to load, manage, analyze, visualize, and query gene expression data.
10. GenMAPPhttp://www.genmapp.org/
GenMAPP enables the visualization of gene expression and genomic data on maps representing biological pathways and groupings of genes. Programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder) are integrated into GenMAP.P
11. GEO: GENE EXPRESSION OMNIBUShttp://www.ncbi.nlm.nih.gov/geo/
GEO is a high-throughput gene expression/molecular abundance data repository, and a curated, online resource for gene expression data browsing, query, and retrieval.
12. GXD: GENE EXPRESSION DATABASEhttp://www.informatics.jax.org/mgihome//GXD/aboutGXD.shtml
The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data available in formats appropriate for comprehensive analysis.
13. HTD: HUMAN TRANSCRIPT DATABASEhttp://www.hgsc.bcm.tmc.edu/HTDB/
HTD is focused on complete or nearly complete human transcript sequences.
14. HuGE: HUMAN GENE EXPRESSION INDEXhttp://132.183.243.28/hio/
The HuGE index provides a comprehensive database of human gene expression.
15. HUGE: HUMAN UNIDENTIFIED GENE-ENCODED DATABASEhttp://www.kazusa.or.jp/huge/
HUGE is focused on long cDNAs (>4 kb) encoding large proteins (>50 kDa).
16. KDGED: KIDNEY DEVELOPMENT GENE EXPRESSION DATABASEhttp://organogenesis.ucsd.edu/
KDGED is a database of gene expression in the developing kidney.
17. MGC: MAMMALIAN GENE COLLECTIONhttp://mgc.nci.nih.gov/
MGC provides full-length open reading frame clones for human, mouse, and rat genes. All sequences are deposited in GenBank and may be purchased from distributors for the IMAGE consortium (American Type Culture Collection, Invitrogen, Open Biosystems)
18. miRNA REGISTRYhttp://www.sanger.ac.uk/Software/Rfam/mirna/index.shtml
A searchable database of published miRNAs.
19. MOUSE GENE EXPRESSION LITERATURE QUERY FORMhttp://www.informatics.jax.org/searches/gxdindex_form.shtml
The Gene Expression Literature Index comprises references that include data on endogenous gene expression during mouse development. For each reference, information on the genes and ages analyzed and assay types used is provided.
20. MOUSE GENOME INFORMATICS GENE EXPRESSION SEARCH TOOLShttp://www.informatics.jax.org/menus/expression_menu.shtml
Tools for searching literature, gene expression data, anatomical structures, and cDNA clones.
21. MPB: MOLECULAR PROBE DATABASEhttp://www.biotech.ist.unige.it/interlab/mpdb.html
Information on a collection of over 4,000 oligonucleotides.
22. NONCODEhttp://noncode.bioinfo.org.cn/
A database of noncoding RNAs (ncRNAs) classified by function, cellular role, and cellular location.
23. PROBEBASEhttp://www.microbial-ecology.de/probebase/
An online resource for rRNA-targeted oligonucleotide probes.
24. READ: RIKEN EXPRESSION ARRAY DATABASEhttp://read.gsc.riken.go.jp/
An integrated system formicroarray data.
25. REFSET OLIGOShttp://www.illumina.com/products/dna/genomesets/reft_set_oligos.ilmn
Oligonucleotide probes for analyzing the expression of 21,000 human genes characterized in the NCBI RefSeq database, including probes to interrogate alternate splice variants.
26. REGULON DBhttp://tula.cifn.unam.mx:8850/regulondb/regulon_doc.table_description
RegulonDB is a relational database centered on information about transcriptional regulation of gene expression and operon organization in E. coli.
27. RELNET: RELEVANCE NETWORKShttp://www.chip.org/relnet/
A tool for the construction of relevance networks from gene expression data (Java).
28. RFAM: NONCODING RNAshttp://www.sanger.ac.uk/Software/Rfam/
A comprehensive collection of noncoding RNA families, represented by multiple sequence alignments.
29. RNAdb: NONCODING RNAshttp://research.imb.uq.edu.au/rnadb/
A comprehensive mammalian noncoding RNA database.
30. SMD: STANFORD MICROARRY DATABASEhttp://genome-www5.stanford.edu/
The Stanford Microarray Database stores raw and normalized data from microarray experiments, as well as their corresponding image files.
31. SPOTFIRE DECISIONSITE FOR FUNCTIONAL GENOMICShttp://spotfire.com/academics/products-fg.htm
A microarray data analysis tool that merges expression results with current biological annotation information.
32. SYMATLAShttp://symatlas.gnf.org/SymAtlas/
A tool for the visualization of tissue-specific gene expression based on comprehensive microarray data from the Novartis Foundation. SymAtlas may be queried by gene or by tissue.
33. TIGR GENE INDICEShttp://www.tigr.org/tdb/tgi/
TIGR gene indices provide annotation on ESTs.
34. UTResourcehttp://bighost.area.ba.cnr.it/BIG/UTRHome/
A database of 5' and 3' untranslated sequences and functional elements of eukaryotic mRNAs.
35. UTRSite http://www2.ba.itb.cnr.it/UTRSite/www/index.php
A database of 5' and 3' untranslated sequences of eukaryotic mRNAs that enables searching any input sequence for the presence of functional motifs..

1. BCCM: BELGIAN CO-ORDINATED COLLECTIONS OF MICRO-ORGANISMShttp://www.belspo.be:80/bccm/
The BCCMTM constitutes four complementary collections and includes over 50,000 strains of bacteria, yeast and filamentous fungi, and 1,500 plasmids.
2. CABRI: FILAMENTOUS FUNGI & YEAST CATALOGShttp://www5.cabri.org/CABRI/cabri-srs-doc/
CABRI (Common Access to Biological Resources and Information Service) provides access to European collections of stocks and related resources.
3. FUNGAL GENETICS STOCK CENTERhttp://www.fgsc.net/
Supplies Neurospora and Aspergillus strains, cloned genes, and gene libraries.
4. FUNGAL GENOMES BLASThttp://seq.yeastgenome.org/cgi-bin/nph-blast-fungal.pl
A form for BLAST comparisons between multiple fungal sequences.
5. MYCORWEBhttp://mycor.nancy.inra.fr/
Information about molecular processes underlying the development of tree roots and ectomycorrhizal symbiosis. Links to EctomycorrhizaDB and PoplarDB as well as molecular ecology databases.
6. NEUROSPORA HOME PAGEhttp://www.fgsc.net/Neurospora/index.html
A resource site for information on the fungus Neurospora.
7. Saccharomyces GENOME DATABASEhttp://www.yeastgenome.org/
A repository for Saccharomyces gene analysis information, including gene expression, comparison, function, and pathway analysis.
8. snoRNAs FROM Saccharomyceshttp://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
A database of small nucleolar RNAs from Saccharomyces cerevisiae.
9. TRIPLES: TRANSPOSON INSERTION PHENOTYPES, LOCALIZATION, AND EXPRESSION IN Saccharomyceshttp://ygac.med.yale.edu/triples/triples.htm
An approach to large-scale functional analysis of gene function based on transposon-tagging and analysis of the subcellular localization of the transposon-tagged proteins.

1. BIOSAPIENS NETWORKhttp://www.biosapiens.info/page.php?page=home
A large-scale effort to annotate genome data by laboratories distributed across Europe, using a virtual genomics annotation environment.
2. COMPARATIVE GENOMICS CENTER (LLNL) http://www.dcode.org/
Online browsers for decoding genomic information based on evolutionary conservation.
3. COMPLETED GENOMES (EBI)http://www.ebi.ac.uk/genomes/
Links to all completed genomes at the European Bioinformatics Institute (EBI) as well as project status and genome annotation tools. Includes recent assembly and pre-assembly data for human, chimp, zebrafish, mouse, anopheles, honeybee genomes.
4. DOGS: DATABASE OF GENOME SIZEShttp://www.cbs.dtu.dk/databases/DOGS/index.php
The Database of Genome Sizes estimates genome sizes using GenBank data.
5. EBI TOOLBOXhttp://www.ebi.ac.uk/Tools/
The European Bioinformatics Institute toolbox provides comprehensive bioinformatics tools for analysis of sequence similarity and function, as well as tools for comparative protein structural analysis, and gene expression profiling.
6. ECR: EVOLUTIONARY CONSERVED REGIONS (LLNL)http://ecrbrowser.dcode.org/
A dynamic whole-genome navigation tool for visualizing and studying evolutionary relationships between vertebrate and non-vertebrate genomes.
7. ENTREZ GENEhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
A unified query environment that links many attributes associated with genes and gene products.
8. GENETESTShttp://www.geneclinics.org/
NIH medical genetics information resource.
9. GENOME CHANNELhttp://compbio.ornl.gov/channel/
Genome analysis tools.
10. GENOME GLOSSARYhttp://www.ornl.gov/sci/techresources/Human_Genome/glossary/
A glossary of genetic terms from the Human Genome program. Includes links to other glossaries, taxonomies, and dictionaries.
11. GENOME MONITORING TABLEhttp://www2.ebi.ac.uk/genomes/mot/
Genome MOT monitors the world wide progress of large (eukaryotic) genome sequencing projects.
12. GENOME REVIEWShttp://www.ebi.ac.uk/GenomeReviews/
Genome Reviews are curated versions of EMBL/GenBank/DDBJ database entries, enhanced with information imported from other data sources such as UniProt, GO, and InterPro.
13. GOLD™ Genomes Online Databasehttp://www.genomesonline.org/
Information on complete and ongoing genome projects around the world.
14. LOCUSLINK (NCBI)http://www.ncbi.nlm.nih.gov/LocusLink/
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites.
15. NCBI SITE MAPhttp://www.ncbi.nlm.nih.gov/Sitemap/index.html
A hierarchical listing of all bioinformatics resources available from the NCBI (National Center for Biotechnology Information), including the NCBI Handbook and tutorials.

1. Arabidopsis FUNCTIONAL GENOMICS CONSORTIUMhttp://www.arabidopsis.org/info/2010_projects/comp_proj/AFGC/
Information on the Arabidopsis Functional Genomics Consortium (dated 2002).
2. BERKELEY DROSOPHILA GENE DISRUPTION PROJECThttp://www.fruitfly.org/p_disrupt/index.html
Information about the Drosophila P element disruption project, and on obtaining P element insertion lines.
3. C. elegans GENE KNOCKOUT CONSORTIUMhttp://www.celeganskoconsortium.omrf.org/
Produces deletion alleles at specified gene targets, based on investigator requests.
4. OMNIBANK (LEXGEN)http://www.lexgen.com/omnibank/overview.php
OmniBank is a library of more than 200,000 knockout mouse embryonic stem cell clones corresponding to mammalian genes. Each OmniBank mouse clone contains a single genetic mutation that may be used to generate gene knockout models for functional analysis.
5. SDG: Saccharomyces Deletion Projecthttp://www-deletion.stanford.edu/cgi-bin/deletion/search3.pl
The Yeast Deletion Database indexes strains made available by Invitrogen, Open Biosystems, and American Type Culture Collection.

1. COMPARATIVE GENOMICS CENTER (LLNL)http://www.dcode.org/
Browsers for visualizing evolutionary conservation of multiple genomes, and for predicting gene regulatory sites using sequence conservation as a filter.
2. ECR BROWSER: EVOLUTIONARY CONSERVED REGIONShttp://ecrbrowser.dcode.org/
A dynamic whole-genome navigation tool for visualizing evolutionary relationships between vertebrate and non-vertebrate genomes.
3. eSHADOW: EVOLUTIONARY PHYLOGENETIC SHADOWING OF CLOSELY RELATED SPECIES (LLNL)http://eshadow.dcode.org/
A tool for comparing closely related species.
4. EVOLUTIONARY BIOLOGY PROJECTShttp://evolve.zoo.ox.ac.uk/
The University of Oxford Evolutionary Biology webpage.
5. GENETIC ANALYSIS SOFTWAREhttp://linkage.rockefeller.edu/soft/
Software for genetic linkage analysis, marker mapping, linkage disequilibrium mapping, and pedigree drawing.
6. MEGA: MOLECULAR EVOLUTIONARY GENETICS ANALYSIShttp://www.megasoftware.net/text/overview.sht
Software for comparative sequence analysis.
7. MIT GENOME CENTER FTP ARCHIVEhttp://www.hgmp.mrc.ac.uk/
Downloadable softwre, including GENEHUNTER (multipoint linkage analysis), MAPMAKER (multipoint genetic analysis).
8. MOLECULAR CYTOGENETICS http://www.sanger.ac.uk/HGP/Cytogenetics/
Protocols and techniques information for molecular cytogenetics.
9. MrBayeshttp://morphbank.ebc.uu.se/mrbayes/
Bayesian inference applied to phylogeny.
10. MULAN (LLNL)http://mulan.dcode.org/
Mulan performs single-coverage local multiple DNA sequence alignments of finished and draft-quality genomic sequences.
11. NCBI TAXONOMYhttp://www.ncbi.nlm.nih.gov/Taxonomy/tax.html/
NCBI's Taxonomy Browser.
12. PAUP: PHYLOGENETIC ANALYSIS USING PARSIMONYhttp://paup.csit.fsu.edu/
Software for inference of evolutionary trees.
13. PHYLIPhttp://evolution.genetics.washington.edu/phylip.html
PHYLIP is a package of programs for inferring phylogenies.
14. PHYLODENDRONhttp://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/
PHYLODENDRON is an application for drawing phylogenetic trees (dated 1999).
15. PHYLPRO: PHYLOGENETIC PROFILEShttp://life.anu.edu.au/molecular/software/phylpro/
PhylPro detects genetic recombination in homologous sequence and graphically displays the coherence of sequence relationships.
16. POPSET (NCBI)http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=popset
Searches sets of DNA sequences collected to analyze the evolutionary relatedness of a population.
17. SPLITSTREE: ANALYZING AND VISUALIZING EVOLUTIONARY DATAhttp://www-ab.informatik.uni-tuebingen.de/software/splits/welcome.html
SplitsTree is based on phylogenetic tree construction methods that consider all possible tree structures supported by the data.
18. TAXONOMY BROWSER (NCBI)http://www.hgmp.mrc.ac.uk/
Taxonomy resources.
19. TREE OF LIFEhttp://tolweb.org/tree/phylogeny.html
Information about phylogeny and biodiversity.
20. TREEBASEhttp://www.treebase.org/treebase/
TreeBASE is a database of phylogenetic information.
21. TREECONhttp://rrna.uia.ac.be/dcse/help/treecon.html
An application for drawing evolutionary trees based on distance matrices calculated from nucleic acid sequences.

1. BDGP: BERKELEY DROSOPHILA GENOME PROJECThttp://www.fruitfly.org/
A repository of Drosophila information, including DNA sequence, gene expression patterns in embryogenesis, cDNAs, transposable elements, SNPs, and comparative genomics.
2. DROSOPHILA GENOME RESOURCES (NCBI)http://www.ncbi.nlm.nih.gov/genome/guide/fly/
A gateway page for Drosophila-related resources.
3. FLYBASEhttp://www.flybase.org/
A portal to Drosophila resources, including maps, genes, gene annotation, anatomy, stocks, and references.
4. FLYBRAINhttp://www.flybrain.org/
An atlas and database of the Drosophila nervous system.
5. FLYMOVEhttp://pbio07.uni-muenster.de/FlyMove/FlyMove%20Neu/Homepage.html
A Drosophila multimedia database, with emphasis on developmental biology.
6. FLYTRAPhttp://www.fly-trap.org/
Flytrap correlates image data, genetic data, and phenotypic data for genetically transformed strains of Drosophila.
7. FLYVIEWhttp://pbio07.uni-muenster.de/FlyView/Home.html
A Drosophila image database.
8. THE INTERACTIVE FLYhttp://www.sdbonline.org/fly/aimain/1aahome.htm

1. CLONERANGER™ http://clones.invitrogen.com/cloneranger.php
Searches all Invitrogen clone collections for cDNAs.
2. CLONES (ATCC)http://www.atcc.org/customPlateOrder/index.cfm
Molecular genomics resources.
3. GENOMECUBE™ (RZPD)http://www.rzpd.de/
Direct access to a multitude of validated material about RZPD products, including full-length clones, expression clones, genomic clones, sequence-verified cDNA clones, and esiRNA resources.
4. I.M.A.G.E. CONSORTIUM (iNTEGRATED MOLECULAR ANALYSIS OF GENOMES AND THEIR EXPRESSION)http://image.llnl.gov/image/html/idistributors.shtml
Information about distributors for the I.M.A.G.E. consortium.
5. INVITROGEN CLONEShttp://clones.invitrogen.com/
Access to the Invitrogen clone collections, consisting of both full-length cDNAs and ESTS.
6. OPEN BIOSYSTEMShttp://www.openbiosystems.com/
Innovative genomic and proteomic resources
7. ULTIMATE™ ORF BROWSERhttp://orf.invitrogen.com/cgi-bin/ORF_Browser
Advanced search for Ultimate™ ORF Clones (full-length sequenced human and mouse open reading frames in Gateway® vectors.

1. 2HAPIhttp://array.sdsc.edu/hapi_web/
2HAPI is a web-based microarray data analysis system that provides tools to browse, visualize, and analyze data obtained from genome-wide gene expression experiments.
2. ARGOhttp://www.broad.mit.edu/annotation/argo/
A tool for visualizing and manually annotating whole genomes (JAVA).
3. BiODS: BIOLOGY-CENTERED INTERFACE SYSTEM DRIVEN BY ONTOLOGIEShttp://www.oriel.org/webservices.htm
A semantic adaptive system that provides transparent access to a variety of databases and analytic tools (JAVA).
4. BIOIMAGE DATABASEhttp://www.oriel.org/images.htm
A database of multidimensional digital images of biological research relevance with descriptive metadata, based on Semantic Web technology.
5. BiOMART (EBI)http://www.ebi.ac.uk/biomart/
A successor to the Ensembl genome database query system, BioMart provides interactive access to Internet bioinformation, and may be used for in house data integration.
6. BIOMOBYhttp://www.biomoby.org/
BioMOBY is a quest for interoperable bioinformatics solutions, including Semantic Web-based solutions.
7. BIOPATHWAYS CONSORTIUMhttp://www.biopathways.org/
The mission of the BioPathways Consortium is to catalyze the emergence and development of computational pathways biology.
8. BioPAX: BIOLOGICAL PATHWAYS EXCHANGEhttp://www.biopax.org/
BioPAX is a collaborative effort to create a data exchange format for biological pathway data.
9. BIOPERL PROJECThttp://www.bioperl.org/
The Bioperl Project brings together developers of open source Perl tools for bioinformatics, genomics, and life science research. The Bioperl server provides an online resource for modules, scripts, and web links for developers.
10. BIOPYTHON PROJECThttp://www.biopython.org/
The Biopython Project makes available Python tools for computational molecular biology. The site provides links to other open bioinformatics projects.
11. BMC BIOINFORMATICShttp://www.biomedcentral.com/bmcbioinformatics
Open access to bioinformatics articles.
12. CLUSTER SOFTWAREhttp://rana.lbl.gov/EisenSoftware.htm
Cluster is a program for analyzing the results of complex microarray experiments.
13. COLLEXIS®http://www.collexis.com/
Applications for making large amounts of unstructured information easily accessible.
14. DAS: DISTRIBUTED ANNOTATION SYSTEMhttp://biodas.org/
A system for exchanging annotations on genomic sequence data.
15. DATABASE MINING WHITE PAPERhttp://www.biodatabases.com/whitepaper01.html
A white paper published by Biodatabases.com, dealing with the ways that genome, gene expression, and proteome database mining contribute to the generation of high-resolution structural and functional maps.
16. DATAMINING LINKShttp://www.gene-chips.com/#Datamining
Links to a collection of datamining tools (dated 2002).
17. E-BIOSCI (EMBO)http://www.e-biosci.org/
A federated network of European bioinformatics platforms.
18. ENCODE: ENCYCLOPEDIA OF DNA ELEMENTS (NHGRI)http://www.genome.gov/10005107
A project to identify all functional elements of the human genome sequence.
19. ENTREZ GENEhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
A unified query environment that links many attributes associated with genes and gene products.
20. EXPRESSION PROFILERhttp://ep.ebi.ac.uk/EP/
Expression Profiler is a set of tools for clustering, analysis, and visualization of gene expression and other genomic data. Includes applications for pattern discovery and visualization, cluster analysis, extraction of regulatory sequences, and study of protein interactions.
21. GENESPRING™http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring
FAQs, tech notes, analysis guides for Silicon Genetics GeneSpring™ software.
22. GENESPRING™ TESTDRIVEhttp://www.silicongenetics.com/cgi/SiG.cgi/index.smf
Downloadable test version of Silicon Genetics GeneSpring™ software.
23. GEO: GENE EXPRESSION OMNIBUS (NCBI)http://www.ncbi.nlm.nih.gov/geo/
A repository of high-throughput gene expression datasets, as well as a curated gene expression data resource.
24. GO: GENE ONTOLOGY CONSORTIUMThe goal of the Gene Ontology Consortium is to produce a controlled vocabulary that may be applied to all organisms. GO provides three networks of annotation based on molecular function, biological process, and cellular localization for each gene.
The goal of the Gene Ontology Consortium is to produce a controlled vocabulary that may be applied to all organisms. GO provides three networks of annotation based on molecular function, biological process, and cellular localization for each gene.
25. GRIDIThttp://www.bsi.vt.edu/ralscher/gridit/index.htm
A diverse set of microarray resources (dated 2002).
26. IHOP: INFORMATION HYPERLINKED OVER PROTEINShttp://www.pdg.cnb.uam.es/UniPub/iHOP/
A network approach to linking literature to genes and building models based on user selections.
27. IN SILICO CLONING TUTORIALhttp://gps.gsc.riken.jp/insilico/insilico_cloning_index.htm
A bioinformatics approach to locating candidate genes in a region defined by quantitative trait loci (QTLs).
28. INTERNET BIOLOGISTShttp://www.internetbiologists.org/
A worldwide network of collaborators in academia and industry, available to participate in and assist with new projects on a volunteer basis.
29. ISB: INSTITUTE FOR SYSTEMS BIOLOGYhttp://www.systemsbiology.org/
The goal of ISB is to apply systems biology to the development of strategies for predicting and preventing disease.
30. KNOWLEDGE-BASED ANALYSIS OF GENE EXPRESSION DATAhttp://www.cse.ucsc.edu/research/compbio/genex/genex.html
An article describing a method for functional classification of gene expression data from microarray hybridization experiments.
31. LION BIOSCIENCE DEMO CENTERhttp://www.lionbioscience.com/solutions/e18200/index_eng.html
Links to bioinformatics demos and white papers.
32. LION BIOSCIENCE DEMO CENTERhttp://www.lionbioscience.com/solutions/e18200/index_eng.html
Demos for bioinformatics software from Lion Bioscience.
33. MAPLE TREEhttp://rana.lbl.gov/EisenSoftware.htm
Maple Tree is a cross-platform visualization tool to graphically browse the results of clustering analyses.
34. http://www.mged.org/
MGED's focus is on establishing standards for microarray data annotation and exchange.
35. MICROARRAY DATA ANALYSIS BIBLIOGRAPHYhttp://www.nslij-genetics.org/microarray/
A collection of papers that emphasize analysis of microarray data.
36. MICROARRAY PROJECT (NHGRI)http://research.nhgri.nih.gov/microarray/
Microarray protocols and analytical resources.
37. MICROARRAYS.ORGhttp://www.microarrays.org/software.html
Software and protocols for microarray analysis.
38. myGRIDhttp://www.mygrid.org.uk/
myGRID consists of middleware for in silico experiments in biology.
39. NCBI HANDBOOKhttp://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=handbook.TOC&depth=2
A guide to the use of NCBI bioinformatics resources.
40. OMNIGENEhttp://omnigene.sourceforge.net/
Omnigene provides middleware for database access, and interfaces for accessing bioinformatics databases.
41. OPENHELIX BIOINFORMATICS TRAININGhttp://www.openhelix.com/ucscmaterials.shtml
OpenHelix provides free training on the use of the UCSC bioinformatics browser, including a pre-recorded tutorial.
42. ORIEL GENE MINING TOOLShttp://www.oriel.org/gene_analysis.htm
A variety of approaches to searching for gene information and correlating putative biological functions from information in the literature.
43. ORIEL: ONLINE RESEARCH INFORMATION ENVIRONMENT FOR THE LIFE SCIENCES (EMBC, EMBO)http://www.oriel.org/text_tools.htm
ORIEL applies Semantic Web-based data-mining methods to bioinformatics databases.
44. PROTEIN SEQUENCE ANALYSIShttp://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj/introfrm.html
A practical guide to bioinformatics.
45. PROTOARRAY™ PROSPECTORhttp://www.invitrogen.com/content.cfm?pageid=10400
A tool for interpretation protein array experimental results.
46. SAGEmaphttp://www.ncbi.nlm.nih.gov/SAGE/
SAGEmap is a resource for the query, retrieval, and analysis of SAGE (serial analysis of gene expression) data from any organism.
47. ScanAlyzehttp://rana.lbl.gov/EisenSoftware.htm
ScanAlyze processes fluorescent images of microarrays.
48. SEQUENCE ANALYSIS WITH DISTRIBUTED RESOURCES (AN ONLINE COURSE)http://bibiserv.techfak.uni-bielefeld.de/sadr/index2.html
An online course on the use of Internet bioinformatics resources to solve basic research problems.
49. SOFTWARE TOOLS (TIGR)http://www.tigr.org/software/
Software systems for gene finding, annotation, alignment, sequencing, finishing, and microarray computution.
50. SPIDEYhttp://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/Spidey/index.html
Spidey is an mRNA-to-genomic DNA alignment program.
51. TAVERNA http://taverna.sourceforge.net/
Software tools to facilitate workflow for e-science.
52. TBR: THE BIOINFORMATICS RESOURCEhttp://www.hgmp.mrc.ac.uk/CCP11/index.jsp
The goal of TBR is to facilitate transfer of bioinformatics knowledge within the UK research community.
53. TREEVIEW http://rana.lbl.gov/EisenSoftware.htm
TreeView is a program for visualizing the results of complex microarray experiments which supports tree-based and image-based browsing of hierarchical trees. TreeView provides multiple output formats for generation of images for publication.
54. VISUALIZATION FOR BIOINFORMATICS (EBI)http://industry.ebi.ac.uk/%7Ealan/VisSupp/
Extensive links to information on microarray data visualization software.
55. XML IN BIOINFORMATICShttp://bio.perl.org/Projects/XML/
A discussion of advantages and disadvantages of using XML as a biological data markup language.

1. BCCM: BELGIAN CO-ORDINATED COLLECTIONS OF MICRO-ORGANISMShttp://www.belspo.be:80/bccm/
A catalog of bacterial strains.
2. CABRI SIMPLE SEARCHhttp://www5.cabri.org/CABRI/cabri-srs-doc/
Catalogs of bacterial strains.
3. CGSC DB WEB SERVERhttp://cgsc.biology.yale.edu/top.html
Information about bacterial strains, mutations, genes, and gene products in the CGSC collection.
4. COMPLETE MICROBIAL GENOMES (NCBI ENTREZ GENOME PROJECT)http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
Information about completed microbial genomes.
5. CYANOBASEhttp://www.kazusa.or.jp/cyanobase/
The genome database for cyanobacteria.
6. DNA STRUCTURAL ATLAS OF Escherichi coli http://www.cbs.dtu.dk/staff/dave/TIGRconf2.html
An examination of the Escherichia coli genome in terms of DNA structural parameters such as base-stacking interactions, flexibility and twist in order to evaluate preferential localization of specific structures within intergenic regions.
7. ECDC: E.coli DATABASE COLLECTIONhttp://www.uni-giessen.de/~gx1052/ECDC/ecdc.htm
Information on E.coli K12, including the map, open reading frames, promoters, and EMBL entries.
8. ECOWEBhttp://bmb.med.miami.edu/EcoGene/EcoWeb/
Information about genes, proteins, and intergenic regions of the E.coli K-12 genome and proteome.
9. EnteriX: BACTERIAL GENOME ALIGNMENTShttp://globin.cse.psu.edu/enterix/
Comparative views of a reference genome with sequences from several related bacteria using three different visualization tools.
10. EMGLIB: ENHANCED MICROBIAL GENOMES LIBRARYhttp://pbil.univ-lyon1.fr/emglib/emglib.html
A database of complete bacterial genomes and the yeast genome.
11. GENPROTEC: E.coli GENOME AND PROTEOME DATABASEhttp://genprotec.mbl.edu/
Annotated information about E. coli K-12, including orthologs, references, functional classification, and SCOP protein superfamily.
12. IS FINDER: INSERTION SEQUENCES DATABASEhttp://www-is.biotoul.fr/is.html
A list of insertion sequences isolated from eubacteria and archae.
13. LBSN: LIST OF BACTERIAL NAMES WITH STANDING IN NOMENCLATUREhttp://www.bacterio.cict.fr/
The bacterial nomenclature.
14. MICROBIAL GENOMES BLAST DATABASES (NCBI)http://www.ncbi.nlm.nih.gov/Microb_blast/unfin_databases.html
BLAST databases of unfinished microbial genome sequences not yet deposited to NCBI.
15. NCCB: NETHERLANDS CULTURE COLLECTION OF BACTERIAhttp://www.cbs.knaw.nl/nccb/
A collection of bacteria, bacteriophages, and plasmids.
16. PATHOGENEhttp://pathogene.swmed.edu/
A CDS (coding sequence) finding and primer design tool for microorganisms.
17. PEDANThttp://pedant.gsf.de/
A genome database that provides exhaustive automatic analysis of bacterial and other genomic sequences by a variety of bioinformatics tools.
18. PSORT-Bhttp://www.psort.org/
Protein subcellular localization in Gram-positive and Gram-negative bacteria.
19. REP-PCR: GENOMIC FINGERPRINTINGhttp://www.msu.edu/user/debruijn/loadr.html
Rep-PCR is a bacterial phylogenetic analysis technique based on genomic fingerprinting.
20. SUBTILIST WWW SERVERhttp://genolist.pasteur.fr/SubtiList/