An Overview of Genome Databases

An Overview of Genome Databases Dave Ussery DTU course #27104 Communicating Science: Comparative Genomics Wednesday, first talk 9 September, 2009 Department of Systems Biology, Technical University of Denmark - or Where can I find up-to-date information about genomes? Center for Biological Sequence analysis Comparative Microbial Genomics group Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark October November Learn tools to compare genomes Use tools to compare genomes Posters due Journal Clubs / podcast Journal Clubs / podcast Journal Clubs / podcast Lectures on how to write papers! Write papers (!) Referee / publish Department of Systems Biology, Technical University of Denmark September Center for Biological Sequence analysis Comparative Microbial Genomics group ฀ ฀ ฀ ฀ ฀ ฀ ฀ ฀ Department of Systems Biology, Technical University of Denmark ฀ ฀ ฀ Center for Biological Sequence analysis Comparative Microbial Genomics group Fasta format >gi|169754007|gb|ACA76706.1| histone family protein nucleoid-structuring protein H-NS MSVMLQSLNNIRTLRAMAREFSIDVLEEMLEKFRVVTKERREEEEQQQRELAERQEKISTWLELMKADGI NPEELLGNSSAAAPRAGKKRQPRPAKYKFTDVNGETKTWTGQGRTPKPIAQALAEGKSLDDFLI GenBank format LOCUS ACA76706 134 aa linear BCT 09-MAY-2008 DEFINITION histone family protein nucleoid-structuring protein H-NS [Escherichia coli ATCC 8739]. ACCESSION ACA76706 SOURCE Escherichia coli ATCC 8739 ORGANISM Escherichia coli ATCC 8739 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia. FEATURES Location/Qualifiers source 1..134 /organism="Escherichia coli ATCC 8739" /strain="ATCC 8739" /db_xref="ATCC:8739" /db_xref="taxon:481805" Protein 1..134 /product="histone family protein nucleoid-structuring protein H-NS" CDS 1..134 /locus_tag="EcolC_1037" /coded_by="CP000946.1:1125675..1126079" /note="PFAM: histone family protein nucleoid-structuring protein H-NS KEGG: sdy:SDY_2859 DNA-binding protein" /transl_table=11 /db_xref="InterPro:IPR001801" ORIGIN 1 msvmlqslnn irtlramare fsidvleeml ekfrvvtker reeeeqqqre laerqekist 61 wlelmkadgi npeellgnss aaapragkkr qprpakykft dvngetktwt gqgrtpkpia 121 qalaegksld dfli // Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark CP000828 Not curated Author submits Only author can revise Multiple records for same loci common Records can contradict each other No limit to species included Data exchanged among INSDC members Akin to primary literature Proteins identified and linked Access via NCBI Nucleotide databases RefSeq NC_009925 Curated NCBI creates from existing data NCBI revises as new data emerge Single records for each molecule of major organisms Limited to model organisms Exclusive NCBI database Akin to review articles Proteins and transcripts identified and linked Access via Nucleotide & Protein databases Department of Systems Biology, Technical University of Denmark GenBank Center for Biological Sequence analysis Comparative Microbial Genomics group Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark ฀ ฀฀฀฀฀ ฀ ฀ ฀ ฀ ฀ Department of Systems Biology, Technical University of Denmark ฀฀ ฀฀ ฀ ฀ ฀ ฀฀฀฀฀ ฀ ฀ ฀ ฀ ฀ ฀ ฀ Center for Biological Sequence analysis Comparative Microbial Genomics group Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark From: tolstoy@ncbi.nlm.nih.gov Subject: [Genomes-announce] [NCBI Genomes] News on completion of the public genome projects Date: 8 September 2009 20:55:04 GMT+02:00 To: genomes-announce@ncbi.nlm.nih.gov Dear colleagues, Please see below the most recent news on completion of the public genome projects Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halomicrobium;Halomicrobium mukohataei DSM 12286 Sequence data files submitted to GenBank/EMBL/DDBJ can be found at: ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halomicrobium_mukohataei_DSM_12286 RefSeq provisional version of the genome can be found at: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Halomicrobium_mukohataei_DSM_12286 _______________________________________________ Genomes-announce mailing list Genomes-announce@ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/mailman/listinfo/genomes-announce Department of Systems Biology, Technical University of Denmark What about other [genome-related] databases? Comparative Microbial Genomics group Center for Biological Sequence analysis Nucleic Acids Research, 2008, Vol. 36, Database issue D1 doi:10.1093/nar/gkm1139 EDITORIAL The 2008 Database Issue of Nucleic Acids Research is the fifteenth in a series dedicated to databases in the field of molecular biology. These databases are essential resources for experimental and computational biologists alike and this compilation provides descriptions and updates of the most important of these databases, and serves to introduce newly compiled resources that provide specialist information in the biological area. The current issue presents 98 new databases (30 more than last year) and updates for 84 existing databases. The 2008 Database Issue is not included in the print subscription to NAR. Instead, the Database Issue is freely available online to all under NAR’s open access model. However, print copies are available for separate purchase by institutions and individuals. After 5 years as the Database Issue Editor I am stepping down. It has been my great pleasure to watch the growth of so many wonderful database resources and to help provide a forum for describing this important work. I am very pleased to announce that Michael Galperin will take over editing the next Database Issue. ALL authors wishing to submit articles for the 2008 Database Issue MUST contact Dr M. Galperin (nardatabase@gmail.com) with a presubmission enquiry, no later than July 1, 2008, to check whether a submission will be suitable for the issue. The pre-submission enquiry must present a working web accessible database for review by the Editor. Articles describing new databases will need to be received by August 15, 2008 at the latest, and should be prepared according to the instructions on the Nucleic Acids Research website (http://nar.oupjournals.org/). Authors who are submitting articles providing update information on databases that have previously been featured in Nucleic Acids Research should note that the deadline for submission of those articles is September 15, 2008. The database issue would not be possible without timely reports from hundreds of reviewers. Thanks to you all! I would also like to thank Deborah Wardle for excellent editorial assistance. Finally, I would like to thank Claire Bird, and the rest of the team at Oxford University Press for producing this important issue. Alex Bateman Department of Systems Biology, Technical University of Denmark Michael Galperin has continued to produce and enlarge the Molecular Biology Database Collection, a compendium of databases that includes all those databases described in Nucleic Acids Research, as well as selected other databases relevant to biologists. NAR Online contains links to all of the databases in the compilation as well as brief summaries of their content. Individuals who wish to have their database listed in the Molecular Biology Database Collection or update a previous submission to the collection should contact Dr Michael Galperin directly (nardatabase@gmail.com). Center for Biological Sequence analysis Comparative Microbial Genomics group Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark Comparative Microbial Genomics group Center for Biological Sequence analysis Department of Systems Biology, Technical University of Denmark