HOME  |  GenomeBank  |  Search  |  Views  |  Datasets  |  Submit your Dataset |  About GenomeMine  |       XML RSS TEXT 1 Title Calculated Composition data for Bacteria : data for all protein genes Date Last Updated 26-06-2005 Curator(s) Haruo Suzuki hsuzuki@uidaho.edu Department of Biological Sciences, University of Idaho http://www.sci.uidaho.edu/biosci/labl/top/ Links Description Composition data calculated by Dr Haruo Suzuki HTML view ?action=composition_all download ?action=composition_all&format=text variables ?action=dataset_variables&table_name=composition_all 2 Title Calculated Composition data for Bacteria : data for ribosomal protein genes Date Last Updated 26-06-2005 Curator(s) Haruo Suzuki hsuzuki@uidaho.edu Department of Biological Sciences, University of Idaho http://www.sci.uidaho.edu/biosci/labl/top/ Links Description Composition data calculated by Dr Haruo Suzuki HTML view ?action=composition_rp download ?action=composition_rp&format=text variables ?action=dataset_variables&table_name=composition_rp 3 Title Calculated Composition data for Bacteria : data for whole genome, RNA genes, and spacers Date Last Updated 26-06-2005 Curator(s) Haruo Suzuki hsuzuki@uidaho.edu Department of Biological Sciences, University of Idaho http://www.sci.uidaho.edu/biosci/labl/top/ Links Description Composition data calculated by Dr Haruo Suzuki HTML view ?action=composition_genome download ?action=composition_genome&format=text variables ?action=dataset_variables&table_name=composition_genome 4 Title Composition Data for Bacteria Date Last Updated 20-03-2005 Curator(s) Haruo Suzuki hsuzuki@uidaho.edu Department of Biological Sciences, University of Idaho http://www.sci.uidaho.edu/biosci/labl/top/ Links G-language http://www.g-language.org/ Description Composition data calculated by Dr Haruo Suzuki including: base usage indices (ryr gac gcc gtc gcs tas Hbu); amino acid usage indices (Haau hydropathy aromaticity); codon usage indices (Hcu Dcu Dsyn Hs Hw Ew enc cbi icdi). Analyses are implemented in a G-language GAE and distributed with the software package at http://www.g-language.org/. HTML view ?action=composition download ?action=composition&format=text variables ?action=dataset_variables&table_name=composition 5 Title Curated ecology for bacteria Date Last Updated 12-12-2004 Curator(s) Dawn Field dfield@ceh.ac.uk Centre for Ecology & Hydrology Jennifer Hughes Jennifer_B_Hughes@brown.edu Brown University Links GenomeMine http://www.genomics.ceh.ac.uk/GMINE Definition of Variables http://www.genomics.ceh.ac.uk/gmine/genomebankbacterialinfo.html Description Curated genomic features and ecological information for bacterial genomes HTML view ?action=BacDec2004 download ?action=BacDec2004&format=text variables ?action=dataset_variables&table_name=BacDec2004 6 Title Curated information for eukaryotic genomes Date Last Updated 01-04-2005 Curator(s) Dawn Field dfield@ceh.ac.uk Centre for Ecology & Hydrology Jennifer Hughes Jennifer_B_Hughes@brown.edu Brown University Links GenomeMine http://www.genomics.ceh.ac.uk/GMINE Description Information curated from the primary genome reports of eukaryotic genomes. HTML view ?action=EukTax download ?action=EukTax&format=text variables ?action=dataset_variables&table_name=EukTax 7 Title Data from the NCBI Genome Project Database for Bacteria Date Last Updated 06-05-2005 Curator(s) Dawn Field dfield@ceh.ac.uk Centre for Ecology & Hydrology Tanya Gray tgra@ceh.ac.uk Centre for Ecology & Hydrology Links NCBI Genome Project http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj Description Contains data retrieved from the NCBI GENOMEPRJ database. HTML view ?action=genomeprj_bacs download ?action=genomeprj_bacs&format=text variables ?action=dataset_variables&table_name=genomeprj_bacs 8 Title Data from the NCBI Genome Project Database for Eukaryotes Date Last Updated 06-05-2005 Curator(s) Dawn Field dfield@ceh.ac.uk Centre for Ecology & Hydrology Tanya Gray tgra@ceh.ac.uk Centre for Ecology & Hydrology Links NCBI Genome Project http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj Description Contains data retrieved from the NCBI GENOMEPRJ database. HTML view ?action=genomeprj_euks download ?action=genomeprj_euks&format=text variables ?action=dataset_variables&table_name=genomeprj_euks 9 Title Data from the NCBI Genome Project Database for Plasmids and Organelles Date Last Updated 06-05-2005 Curator(s) Dawn Field dfield@ceh.ac.uk Centre for Ecology & Hydrology Tanya Gray tgra@ceh.ac.uk Centre for Ecology & Hydrology Links NCBI Genome Project http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj Description Contains data retrieved from NCBI GENOMEPRJ database. HTML view ?action=genomeprj_other download ?action=genomeprj_other&format=text variables ?action=dataset_variables&table_name=genomeprj_other 10 Title Genomic Features (calculated data for bacteria, organelles, plasmids, viruses and viroids) Date Last Updated 28-02-2006 Curator(s) Tanya Gray tgra@ceh.ac.uk Centre for Ecology & Hydrology Links GenomeMine http://www.genomics.ceh.ac.uk/GMINE Description Features extracted and calculated from Genbank genome annotations HTML view ?action=genomic_features download ?action=genomic_features&format=text variables ?action=dataset_variables&table_name=genomic_features 11 Title GOLD Genomes OnLine Database Date Last Updated 27-02-2006 Curator(s) Nikos Kyrpides NCKyrpides@lbl.gov DOE Joint Genome Institute Links GOLD http://www.genomesonline.org Description Information extracted from the table of completed genome projects for bacteria and eukaryotes curated by Nikos Krypides from his GOLD database. Post data retrieval edits by Tanya Gray (tgra@ceh.ac.uk) :- Genome size for Candida glabrata CBS138 retrieved from NCBI Genome Project database. Genome size for Mus musculus, Homo sapiens, Danio rerio (Zebrafish), and Rattus norvegicus (Rat) retrieved from Ensembl database (ensembl.org). NC number changed for record Gc00264 (Pseudomonas syringae syringae B728a) from NC_007004 (which no longer exists in NCBI genbank) to NC_007005. HTML view ?action=gold_genomes download ?action=gold_genomes&format=text variables ?action=dataset_variables&table_name=gold_genomes 12 Title Microsatellites in Microbial Genomes Date Last Updated 01-04-2005 Curator(s) Milo Thurston mith@ceh.ac.uk Centre for Ecology & Hydrology Links Msatfinder http://www.genomics.ceh.ac.uk/msatfinder Description The total number of mono- to hexanucleotide microsatellites longer than 15, 8, 8, 8, 8, 8 repeat units for bacteria, viruses, plasmids, and organellar genomes. HTML view ?action=microsat download ?action=microsat&format=text variables ?action=dataset_variables&table_name=microsat 13 Title Orphan Gene Frequencies in Bacterial Genomes Date Last Updated 20-05-2005 Curator(s) Gareth Wilson gawi@ceh.ac.uk Centre for Ecology & Hydrology Links OrphanMine http://www.genomics.ceh.ac.uk/orphan_mine/orphan_home.php Description Dataset 1 --------- 150 complete bacterial genomes comprising 150 bacterial species/strains were used for this data analysis. Genome files (.faa) format were obtained from the NCBI and were used to generate a SELF BLAST database. Every predicted protein from every genome was blasted against every predicted protein from every genome, using the parameters displayed below: blastall -p blastp -d SELF_blast_database -e 1e-3 -b 500 -f 9 -F 'mS' -M BLOSUM45 Predicted proteins that did not find a statistically significant match (using an e-v alue threshold of 10-3) were designated as orphans. This process was performed by the suite of perl scripts known as QuickMine. Dataset 2 --------- Same as Dataset 1 except predicted proteins that were < 150 amino acids in length or contained regions of low complexity were removed. Dataset 3 --------- Same as Dataset 1 except 122 complete bacterial genomes comprising 122 bacterial species were used for this data analysis. Unlike Dataset 1 & 2 the orphans in this analysis are species specific. The first genome to be sequenced from each species was used to represent the species. Dataset 4 --------- Same as Dataset 3 except predicted proteins that were < 150 amino acids in length or contained regions of low complexity were removed. HTML view ?action=bacteria_orphan_genes download ?action=bacteria_orphan_genes&format=text variables ?action=dataset_variables&table_name=bacteria_orphan_genes 14 Title Swytch - prokaryotic contingency loci with microsatellites Date Last Updated 15-11-2005 Curator(s) Paul Swift pswi@ceh.ac.uk Centre for Ecology & Hydrology Links Swytch http://www.genomics.ceh.ac.uk/lab/swytch.php Description Each bacterial genome is categorised according to whether it has known (yes) or putative (putative) contingency loci containing microsatellites. Evidence is taken from the primary literature and if the associated reference is a primary genome report it is marked 'genome'. This minimal list of references is far from comprehesive. To date, we have not found evidence in the literature support the presence of such loci in the genomes marked as lacking such loci ('no') although these could exist. HTML view ?action=swytch download ?action=swytch&format=text variables ?action=dataset_variables&table_name=swytch 15 Title Taxonomy data for bacteria Date Last Updated 01-10-2004 Curator(s) Dawn Field dfield@ceh.ac.uk Centre for Ecology & Hydrology Links NCBI Taxonomy http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy Description Curated taxonomy based on NCBI taxonomy. HTML view ?action=bactax download ?action=bactax&format=text variables ?action=dataset_variables&table_name=bactax 16 Title Taxonomy data for organelles Date Last Updated 01-10-2004 Curator(s) Milo Thurston mith@ceh.ac.uk Centre for Ecology & Hydrology Links NCBI Taxonomy http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy Description Curated by Milo Thurston. Curated taxonomy based on NCBI taxonomy. HTML view ?action=orgtax download ?action=orgtax&format=text variables ?action=dataset_variables&table_name=orgtax 17 Title Taxonomy data for plasmids Date Last Updated 01-10-2004 Curator(s) Adrian Tett adet@ceh.ac.uk Centre for Ecology & Hydrology Links NCBI Taxonomy http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy Description Curated by Adrian Tett. Curated taxonomy based on NCBI taxonomy. HTML view ?action=plasmidtax download ?action=plasmidtax&format=text variables ?action=dataset_variables&table_name=plasmidtax 18 Title Taxonomy data for viruses, phages, and viroids Date Last Updated 01-10-2004 Curator(s) Milo Thurston mith@ceh.ac.uk Centre for Ecology & Hydrology Links NCBI Taxonomy http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy ICTV http://www.ncbi.nlm.nih.gov/ICTVdb/ Description Data retrieved from NCBI Genbank and ICTV. Additional curation by Milo Thurston. HTML view ?action=virtax download ?action=virtax&format=text variables ?action=dataset_variables&table_name=virtax