Using BacMap

Browsing Genomes

A complete listing of the genomes in the BacMap database is available on the BacMap homepage. Several data fields are available in the table and in each row there are six icons for navigation to tools and maps for further exploration.

Searching for Genomes

Searching for genomes can be accomplished using the search box above the table of genomes on the homepage. This search box moves to the top of the page on any other page for easy access.

Search Syntax

Advanced searches can be accomplished using wildcard symbols '*' at the start or end of words, '|' for 'boolean or', '-' or '!' for negation, and '()' for grouping. See the examples below for how these symbols can be used.

There are four categories to search for genomes:

  • Gene/Protein Names

    Use this option to search for genomes using names of genes and gene products that you are interested in.

  • Genus/Species/Strain

    Use this option to search for genomes for a particular type of bacteria. For example to search for bacteria of the genus Bacillus but exclude the species anthracis and cereus

    The next example finds genomes from a specific strain

  • Text in Biocard

    This option is a more general search, it finds genomes based on keywords in information about the organism, and the genome.

    For example, to find genomes related to fruit disease or vegetable disease.

  • Metabolic Pathway

    Use this option to search for genomes that are involved in a specific metabolic pathway using the name of the pathway.

    For example to find genomes related to fatty acid, butanoate and propanoate pathways

Filtering The Genome List

The genomes listed on the homepage can be filtered using the menu on the left hand side of the page. Select filters from the drop down menues and then click the filter button at the bottom of the menu. Note that you can also filter the results from a search. The filter is reset when you do a new search or hit the reset button.

Blasting Genomes

BLAST Search The blast search button located next to the search box opens a new page with a form that allows for blast searching within the results of a genome search and/or filter.

Genome Maps

In the table listing their are links to 3 maps available by clicking on the corresponding icons.

  • Gene/Protein Map

    Displays the map for the chromosome. The map can be zoomed by clicking the tick marks or by using the navigation buttons. Gene labels, which are drawn when the map is zoomed, are hyperlinked to textual gene annotations.

  • tRna/rRNA Maps

    Displays the map of tRNA/rRNA for the chromosome.

  • Prophage Maps

    Displays the maps of the prophages in the genome. A brief summary, a detailed summary, and an image are available.

Flash requirements: The latest version of flashplayer is required to use the prophage map in some browsers such as Safari. If you are experiencing technical difficulties please upgrade to version 11. Get the latest version here.

Genome Tools

Also in available in the table listing the genomes are a set of tools to further explore the genome.

  • Text Search

    Displays the text search page for the genome. This search compares a supplied query to the contents of several fields in the complete collection gene annotations associated with the chromosome and returns a list of genes relevant to the query.

  • Blast

    Displays the BLAST search page for the genome. This search compares a supplied sequence to the protein sequences, gene sequences, or genomic sequence corresponding to the chromosome. Several options are available for specifying the search type and search parameters. Results are returned in the form of a graphical map and textual alignments. As with the text search, hyperlinks are provided for navigation to BacMap content related to the BLAST hits.

  • Stats

    Displays a page containing several graphs depicting proteome and genome composition.