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Multi-Species Portals
Linkpage 1 - Genome Channel (ORNL)	Genome Channel, developed by the Oak Ridge National Laboratory (ORNL) provides a vast overview of sequencing projects in many organisms (especially bacterial). From eukaryotes, only human, mouse and yeast available. BLAST and keyword search possible.
Linkpage 2 - GOLD - Genomes OnLine Database (Lawrence Berkeley Laboratory and others)	The Genomes OnLine Database (GOLD) is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world. GOLD provides the largest available and most detailed monitoring of genome sequencing projects.
Ensembl (EBI + Sanger) including: TraceView	Ensembl is a joint project between EMBL-EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. 1. Ensembl Genomes: Starting at the homepage, there is access to a variety of organism specific genomes like Human, Mouse, Drosophila, Zebrafish, and Mosquito. In principle, similiar remarks are valid also here as stated for the Ensembl human genome, refer to this section. 2. TraceView: the Ensembl trace repository provides a permanent archive for single pass DNA sequencing reads and associated traces and quality values. You may search the whole archive or subsets using SSAHA, a new fast equivalent of BLAST, or download sets of read sequences in fasta format and associated quality values by FTP.
HGSC - Human Genome Sequencing Center (Baylor College of Medicine)	The Human Genome Sequencing Center (HGSC) at Baylor College of Medicine is involved in many genomic and cDNA sequencing projects. The "Overview" page provides access to all these projects, including species like Human, Mouse, Rat, Drosophila, Rhesus monkey (Macaca mulatta), Chimpanzee, and more.
NCBI - multispecies genome resources (NCBI) including: Genomic Biology Entrez Genome Entrez Genome Project Trace Archive	1. Genomic Biology: A good site to start with when looking for genomic data from various organisms like Human, Mouse, Rat, Zebrafish, Drosophila, Plants, Microbial Genomes, Malaria, and Retroviruses. The links lead to access of NCBI-based software and tools and to other non-NCBI genome databases. 2. Entrez Genome provides a complete list of all eukaryote sequencing efforts for which genomic data is publicly available. This includes large-scale, small-scale genome sequencing projects, as well as EST, GSS, or cDNA sequencing projects. 2.1. Entrez Genome - Microbial genomes is a linkpage to numerous microbial genome projects. 2.2. Entrez Genome - Plant Genomes Central: Collection of plant genome sequencing projects. 3. Entrez Genome Project: The NCBI Entrez Genome Project database is intended to be a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organism-specific overviews that function as portals from which all projects in the database pertaining to that organism can be browsed and retrieved. For example, you will find all information regarding the human genome project on this project page. Note: Although the Entrez Genome Project database does not include viral genome sequencing projects, data from those projects are submitted to GenBank and are available in the Entrez Nucleotide and Entrez Genome databases. 4. The Trace Archive has been developed to store the raw genomic data underlying all of the sequence generated by genome projects. This archive is exchanging data regularly with the Ensembl Trace Server. You can BLAST these sequences with MegaBLAST and Cross species MegaBLAST. The latter version is designed specifically to identify diverged sequences with a low degree of identity, where the standard MegaBLAST is not effective.
TIGR genome resources (TIGR, Rockville, MD, USA) including: TIGR Genome Projects TIGR CMR - Comprehensive Microbial Resource TIGR UFMG - Unfinished Microbial Genomes TIGR Eukaryotic Projects TIGR Parasites Databases TIGR Fungal Databases	1. TIGR 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. Anonymous FTP access to sequence data is also provided. 2. TIGR CMR (Comprehensive Microbial Resource): CMR is a tool that allows the researcher to access all of the bacterial genome sequences completed to date. For each genome not sequenced at TIGR two kinds of annotation are displayed: the Primary annotation taken from the genome sequencing center and the TIGR annotation generated by an automated annotation process at TIGR. 3. TIGR Unfinished Microbial Genomes (UFMG): lists of genomes currently being sequenced and also lists of completed microbial genomes. You may also run a BLAST search on the unfinished genomes. 4. TIGR Eukaryotic Projects: lists of eukaryotic genome sequencing projects at TIGR. 5. TIGR Parasites Databases: Links to TIGR sequencing projects completed and underway as well as links to related world-wide sequencing efforts of a series of parasite species. 6. TIGR Fungal Databases: Fungal genomes that are in the process of being sequenced. 7. TIGR Gene Indices: Integrating data from international EST sequencing, genome sequencing and gene research projects, Gene index are an analysis of transcribed sequences represented in the world's public EST data. Please refer to this main description of the TIGR Gene Indices !
UCSC (University of California, Santa Cruz) including: BLAT UCSC Genome Browser Gateway	1. The UCSC BLAT program allows a very fast access to the growing number of genome databases maintained at UCSC. BLAT uses query sequences to quickly find sequences of 95% and greater similarity of length 40 bases or more. The available species include Human, Mouse, Rat, Drosophila, C.elegans, Fugu, SARS, and more. Please refer to this main chapter describing BLAT. 2. UCSC Genome Browser Gateway (multi-species): Here, you can browse all the listed species by gene names, keywords, accession numbers, cytogenetic positions, author names (submitters), words like "zinc finger" or "huntington", and many more. In principle, it is the same site and interface as for the human genome, so please refer to the main section of the UCSC Genome Browser for a detailed description.

Single Species
Bos taurus (Cow) - genome resources	1. Bovine Genome Project (BCM): The human genome sequencing center at Baylor College of Medicine is working to sequence and annotate the genome of the cow. You can BLAST these genomic data (only BLASTN supported). 2. BLAST Bos taurus UniGene (EST clusters) at Embnet.ch.
C.elegans (Worm) - genome resources including: WormBase (consortium) Proteome BioKnowledge Library (Incyte)	1. WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. Founded in 2000, the WormBase Consortium of CalTech, Wellcome Trust Sanger Institute (WTSC), Cold Spring Harbor (CSHL), and the Washington University Genome Sequencing Center. Note: WormBase can be queried using the BioMart data mining tool. Please refer also to the section WormBase MartView. 2. The so-called Proteome BioKnowledge Library contains extensive yeast and worm genome (proteome) information; (YPD stands for yeast protein database; WormPD stands for C.elegans protein database); NOTE: These databases are now part of Incyte Genomics, access needs (free) registration: www.incyte.com/control/tools/proteome Login 3. You may also BLAST against the C. elegans genome starting from the "eukaryotic genomes selection page"at NCBI and choosing the C. elegans genome. 4. You may also BLAST against the C. elegans genome at Embnet.ch. 5. You can also perform BLAT on the C.elegans genome at UCSC !
Danio rerio (Zebrafish) - genome resources	1. The NCBI Zebrafish Genome Resources page brings together information on diverse zebrafish-related resources from multiple centers. 2. You can BLAST the Zebrafish genome at NCBI. You can choose between different databases (mRNA, EST, HTGS, Reference proteins...). 3. You can access the zebrafish genome at the Ensembl Site (BLAST, keyword search, chromosome browser, etc.) 4. BLAST Zebrafish UniGene (EST clusters) at Embnet.ch.
Drosophila melanogaster (Fruitfly) - genome resources including: FlyBase (consortium)	1. FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. It includes data from the Drosophila Genome Projects and data curated from the literature. 2. The drosophila genome is also available from the Ensembl website ! 3. NCBI provides a genome browser and a BLAST option for the drosophila genome. 4. You may also BLAST the Drosophila genome starting from the "eukaryotic genomes selection page" at NCBI and choosing the Drosophila genome. 5. You may selectively BLAST Drosophila ESTs at Embnet.ch. 6. You can also perform BLAT on the Fruitfly genome at UCSC !
Macaca mulatta (Rhesus monkey) - genome resources	1. At HGSC, you will find an overview of the Rhesus monkey genome project, with several links. 2. Rhesus monkey genomic sequences are blastable at the NCBI Trace archive, using Cross-species Mega BLAST or "normal" Mega BLAST. 3. It is now (May 2005) possible to perform BLAT search on the Rhesus monkey genome. Mmul_0.1 (UCSC version rheMac1) is a preliminary assembly. 4. The Rhesus monkey genome is also available from the Ensembl website !
Mus musculus (Mouse) - genome resources including: MGI - Mouse Genome Informatics (Jackson Laboratory, Maine, USA) MGD - Mouse Genome Database (Jackson Laboratory, Maine, USA) GXD - Gene Expression Database (Jackson Laboratory, Maine, USA) MGS - Mouse Genome Sequence Project (Jackson Laboratory, Maine, USA)	1. MGI (Mouse Genome Informatics) is maintained at Jackson Laboratory, Maine, USA and collects all data about mouse genes, nomenclature, map positions, individual ESTs etc. The main projects contributing to this resource are listed on this MGI Overview page: 1.1. MGD(Mouse Genome Database) includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. (See About MGD.) 1.2. GXD (Gene Expression Database) integrates different types of gene expression information from the mouse and provides a searchable index of published experiments on endogenous gene expression during development. The GXD-Gene Expression page allows to query mouse expression data via different options. 1.3. MGS (Mouse Genome Sequence Project): The goal of the MGS project is to integrate emerging mouse genomic sequence data with the genetic and biological data available in MGD and GXD. MGS supports the MouseBLAST server as a sequence-level entry point into the MGI Database. Typical MGI accessions: refer to section MGI IDs. 2. The mouse genome is also available from the Ensembl website ! 3. A good site for data integration is the Mouse genome resource page at NCBI. 4. You can also BLAST the mouse genome at NCBI ! 5. You can also perform BLAT on the mouse genome at UCSC ! In the dropdown menu "Freeze" choose the desired data freeze ! NOTE: If the BLAT links are unstable, launch the BLAT search starting from the UCSC homepage by choosing the organism and the link "Blat". 6. You may also try to SSAHA search the mouse genome. SSAHA is a software tool for very fast matching and alignment of DNA sequences. Please refer to this main description of SSAHA. 7. BLAST Mouse UniGene (EST clusters) at Embnet.ch.
Pan troglodytes (Chimpanzee) - genome resources	1. The NCBI Taxonomy Browser provides good insight not only into the evolutionary lineage but collects many links concerning the chimp sequencing projects. 2. The chimp genome is also available from the Ensembl website. 3. It is also possible to BLAT search the chimpanzee genome at UCSC.
Rattus (Rat) - genome resources including: RGD - Rat Genome Database (Wisconsin Medical College)	1. The rat genome resources page of NCBI brings together information on diverse rat-related resources from multiple centers: sequence, mapping and clone information. 2. You can BLAST the rat genome at NCBI. 3. The Rat genome database (RGD) is maintained at Wisconsin Medical College and is the primary repository for rat genomic data. The major new resource in v2.0 is VCMap (Virtual Comparative Map) and the comparative maps between Rat, Mouse and Human that are based on the VCMap algorithm. 4. The University of Iowa collects data of the Rat EST Project; corresponds to the TIGR Clusters, but NO consensus sequence; some sequences are only available here. 5. The TIGR Rat Gene Index collects Rat EST and corresponding genomic data. 6. BLAST Rat UniGene (EST clusters) at Embnet.ch. 7. It is also possible to BLAT search the rat genome at UCSC.
Saccharomyces cerevisiae (Bakers Yeast) - genome resources including: CYGD - Comprehensive Yeast Genome Database (MIPS, Munich, Germany)	1. The CYGD - Comprehensive Yeast Genome Database, maintained at MIPS, Munich, Germany, presents a comprehensive database which summarizes the current knowledge regarding the more than 6000 ORFs encoded by the Yeast Genome. 2. You can BLAST the Yeast Genome at NCBI, starting from the "BLAST eukaryotic genomes" - BLAST pages. 3. You can BLAST the yeast genome at Embnet.ch. 4. You can BLAT search the yeast genome at UCSC.
Sus scrofa (Pig) - genome resources	1. The pig genome resources page at NCBI provides a good starting point for information regarding the pig genome data. This homepage brings together information on porcine-related resources from NCBI and the pig research community. 2. The Entrez Genome Project page specific for the Pig genome provides direct links to e.g. all pig-derived sequences stored, like EST, mRNA, protein, and genomic. 3. The TIGR Pig Gene Index provides access to pig EST clusters including the "Tentative Consensus" (TC) sequences. 4. The pig ESTs are also clustered in UniGene (without attempt to produce contig sequences). NOTE (June 2005): There is NO Ensembl database and NO BLAT search option for the pig genome, yet.
Xenopus (Clawed Frog) - genome resources	1. The Sanger Center provides a BLAST server which allows a restricted search in the Xenopus tropicalis or Xenopus laevis EST database prepared from the EMBL database. 2. NCBI UniGene provides clusters of Xenopus laevis ESTs. 3. You can BLAST Xenopus UniGene at Embnet.ch ! 4. You can BLAT search the genome of Xenopus tropicalis.