MicrobesOnline Comparative Genomics Database

Default Boolean Operator: Terms in a search string will be connected by the AND operator, EXAMPLE: searching genomic melanoma will produce the same results as genomic AND melanoma .
AND, OR, NOT: Combine terms in a search with the boolean operators AND (to add specificity), OR (to broaden), or NOT (to eliminate a term). Operators must be capitalized (all other search terms are not case-sensitive).
Wild Card: Add wild card symbols * (open-ended) and ? (single character) to truncate terms. EXAMPLE: searching gen* shows results for 'gene', 'genetic', 'genomic, etc. Searching gene? returns results for 'gene' or 'genes' but not for 'genome'.
Phrase Searching: Enclose search in quotation marks "keyword or search term" to search for an exact phrase. EXAMPLE: "transcription factors" returns results for records where transcription is immediately followed by the word factors .
Diacritics: Words containing diacritics translate those characters to non-diacritic form. EXAMPLE: massague returns results for Massague&#769 .
Filter by: Located on the homepage (left panel), use filters to search for records or narrow the search. From search results page, filters can be removed by clicking on the term at the top of the page.

UID: 10391

Publisher(s): Virtual Institute for Microbial Stress and Survival

Description: The MicrobesOnline genome database contains over 1000 prokaryotic genomes. Genomes were last updated in late 2011 and no further database updates are planned. All genomes are analyzed through the VIMSS genome pipeline. We use publicly available sequence analysis tools and databases to search for homologs (NCBI BLAST, UCSC Blat, SwissProt, COG) and protein domains (HMMer, InterPro), to assign gene ontologies (Gene Ontology Consortium) and EC numbers and to map the metabolic pathways (KEGG). We then link the orthology relationships between genes and predict operon structures. Most genome data is downloaded from RefSeq. When an incomplete genome is directly downloaded from a sequencing center, we submit the genome sequence to RAST for automated annotation. For all genomes, we also search for CRISPR regions using PILER-CR and CRT.

Subject(s)

Access via MicrobesOnline
Access Restrictions: Free to All

Free to all with registration

Application Required
Access Instructions: Publicly accessible online database of prokaryotic genome analysis as well as notes on how to connect to and run SQL queries against a public read-only version of the data (available by request of help@microbesonline.org as of April 5, 2018). Some of the datasets require a free registration in order to view.
Associated Publications: Bacusmo J, Orsini S, Hu J, et al. The t(6)A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans. RNA Biology. 2018; 15(4-5):508-517.
Dataset Format(s): Plain Text

Do you have or know of a dataset that should be added to the catalog? Let us know!