Genome databases (Tripal pages)

Access

A Tripal database is available for each species of the Phaeoexplorer project, containing all strains of the same species.

A link to the genome database (GGA / Tripal) is available at the top of the organism page on the website:

Tripal Home page

The Tripal home page summarises all available organisms and analyses for each species.

On this page you can see the number of sequences/features and some basic information about the analyses and the organisms.

Search

Search for a feature

The features (mRNAs and polypeptides) can be:

• searched via the search box, by its ID or one of its properties (e.g. Ec32 ortholog description)
• accessed by clicking on the Features dropdown menu under the organism's name (leftmost of the top menu)

Advanced Search Tips

Wildcard search with *

Examples:

• *transferase (matches: acyltransferase, sulfotransferase, methyltransferase, ...)
• *F_contig199.* (matches all features on contig199 of the female genome)

Fuzzy search

When you don't know how to exactly spell the keywords, you can use fuzzy search. Fuzzy search allows you to search for similar words. You use the ~ character at the end of your keyword for fuzzy search (keyword~).

Examples:

• transferaase~ (matches: transferase)
• acltransferase~ (matches: acyltransferase)

Boolean operators

+ and -: + means must be present; - means must not be present

Example:

+transferase -acyl (includes the word transferase, excludes the word ̀acyl)

AND, OR, NOT operator and combination search

Example:

transferase AND (acyl OR glycosyl) NOT "family 31"

mRNA pages

On each mRNA page, a left menu is displayed with the following sections:

• Overview: name and ID
• Alignments: gives direct access to the mRNA in the genome browser
• Analyses: list of analyses linked to this mRNA
• Properties: list of properties
• Relationships: links to related features (polypeptide, CDS, UTR, ...)
• Sequences: where you can get the nucleic acid and protein sequences